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ab initio:
From the beginning (Latin)
ab initio
protein modeling:
3D structure from sequence without using a homologous model/ template; this
technology is not at the stage of being broadly applicable to drug discovery.
CHI Structural
proteomics report
Ab initio
methods use the physiochemical properties of the amino acid sequence of
a protein to literally calculate a 3D structure (lowest energy model) based
on protein folding. As opposed to determining the structure of an entire
ab initio methods are typically used to predict and model
protein folds (domains). This method is gaining considerably, in part due
to the development of novel mathematical approaches, a boost in available
computational resources (for example, tera- and pentaFLOPS supercomputers),
and considerable interest from researchers investigating protein- ligand
(or drug) interactions. Christopher Smith "Bioinformatics,
Genomics, and Proteomics" Scientist 14[23]:26, Nov. 27, 2000 http://the-scientist.com/yr2000/nov/profile_001127.html
terms protein structure prediction
ab initio protein
structure prediction:
Prediction of
a proteins structure based on amino acid sequence alone that is, without
mapping the structure to structures of known sequences.
Broader term: protein structure prediction
with ab initio). Narrower term (compared with structure prediction)
ab initio
quantum mechanical methods:
Methods of quantum
mechanical calculations independent of any experiment other than the determination
of fundamental constants. The methods are based on the use of the
full Schrödinger equation to treat all the electrons of a chemical
system. In practice, approximations are necessary to restrict the complexity
of the electronic wave function and to make its calculation possible. (Synonymous
with non- empirical quantum mechanical methods.) IUPAC Computational
ab initio
quantum mechanical modeling: The application
of ab initio modelling cross diverse fields such as condensed matter
physics, materials science and chemistry has been demonstrated over the past 10 years.
... The recent completion of the Human Genome Project will offer an unprecedented
number of protein receptors and enzymes as targets for pharmacological
intervention in disease processes. However, before this wealth of information
can be used to develop pharmaceuticals, an understanding of the biochemistry
of the newly identified proteins and their interactions must be obtained.
First principles quantum mechanical modelling will play an important role
in this process. [Matthew
Segall, Ursula Röthlisberger, Paolo Carloni, CECAM/Psi-k Workshop: Ab Initio
Modelling in the Biological Sciences Lyon, France 11-13 June 2001] http://www.tcm.phy.cam.ac.uk/~mds21/Workshop2001/
annotation- proteins:
Macromolecular structure determination is moving from a
functionally driven initiative to include a genomically driven initiative
(structural genomics) where structures are determined based on what is known
from a target sequence alone. The resultant structures may be structurally and
functionally uncharacterized. Systematic Protein Annotation and Modeling (SPAM)
is a multi-institutional initiative to make better use of target sequences and
structures. SPAM includes new algorithms for the study of sequence-sequence,
sequence-structure and structure-structure and deployment of these methods in
resources available to the community Systematic Protein Annotation and
Modeling Skaggs School of Pharmacy and Pharmaceutical Sciences and the San
Diego Supercomputer Center (SDSC) at the University of California San Diego
(UCSD), the Keck Graduate Institute (KGI) and the Burnham Institute (TBI).
protein - dictionary-driven
many years, computational methods seeking to automatically determine the
properties (functional, structural, physiochemical, etc.) of a protein directly
from sequence have been the focus of numerous research groups, including ours.
By general admission, this is a difficult problem and the methods that have been
proposed over the years typically concentrated on the analysis of individual
genes. With the advent of advanced sequencing methods and systems, the number of
amino acid sequences and fragments being deposited in the public databases has
been increasing steadily. This in turn generated a renewed demand for automated
approaches that can quickly, exhaustively and objectively annotate individual
sequences as well as complete genomes. In this paper, we present one such
approach. The approach is centered around and exploits the Bio- Dictionary, an
exhaustive collection of amino acid patterns (referred to as seqlets)
that completely covers the natural sequence space of proteins to the extent that
this space is sampled by the currently available public databases. Isidore Rigoutsos,
Tien Huynh, Laxmi P. Parida, Daniel E. Platt, Aris Floratos, Dictionary
Driven Protein Annotation, Nucleic Acids Research, 30 (no 17) 3901- 3916,
candidate proteins:
NIGMS (part of NIH) is supporting
research on identifying candidate proteins and their genes, including those that
cause variations in human drug metabolism, transport, distribution, and
excretion (for both small organic molecules and macromolecular drugs such as
peptides and oligonucleotides), that may play a role in determining individual
variations in drug responses and candidate proteins and their genes, including
those that are direct targets for drug action (e.g., receptors, enzymes,
signal transducing molecules, regulatory factors), that may play a role in
determining individual variations in drug responses. National Institute of
General Medical Sciences, Recommendations of the NIGMS Working Group --
Understanding Individual Variations in Drug Responses: From Phenotype to
Genotype , June 9-10, 1998, Bethesda MD http://www.nigms.nih.gov/news/reports/pharmacogenetics.html
terms: Pharmacogenomics
Critical Assessment of Techniques for Protein Structure
Alignment Protein Structure Prediction Center, Lawrence Livermore National
Lab, US http://predictioncenter.llnl.gov/
Links to CASP meetings results and information on "Ten most wanted"
proteins solicitation.
comparative modeling: See homology
comparative proteomics:
C. elegans proteome was used
as an alignment template to assist in novel human gene identification
Among the available 18,452 C. elegans
protein sequences, our results
indicate that at least 83% had human homologous genes, with 7954 records
of C. elegans proteins matching known human gene transcripts. [CH
Lai et al "Identification of Novel Human Genes Evolutionarily Conserved
in Caenorhabditis elegans by Comparative Proteomics" Genome Research
10(5): 703-713 May 2000] Related terms Functional
Genomics glossary comparative genomics, evolutionary
biophysics: Activities of the Theoretical and Computational Biophysics
Group center on the structure and function of supramolecular systems in the
living cell, and on the development of new algorithms and efficient computing
tools for structural biology. The Resource brings the most advanced
molecular modeling, bioinformatics, and computational technologies to bear on
questions of biomedical relevance. Theoretical and Computational Biophysics
Group, Univ. of Illinois Urbana Champaign, About the Group http://www.ks.uiuc.edu/Overview/intro.html
research focuses on the modeling of large macromolecular systems in realistic
environments. These efforts have produced insight into biomolecular processes
coupled to mechanical force, bioelectronic processes in metabolism and vision,
and the function and mechanism of membrane proteins. Theoretical and
Computational Biophysics Group, Univ. of Illinois Urbana Champaign,
Emerging Studies, http://www.ks.uiuc.edu/Research/Recent/
computational proteomics: Large- scale generation and analysis of 3D
and 4D protein structural information and the application of structural
knowledge across all life science disciplines. [Edward T. Maggio, Kal Ramnarayan
"Recent developments in computational proteomics" Trends in
Biotechnology 19 (7): 266- 272 July 2001]
While proteomic studies
initially focused largely on expression and protein identification, progress in
these areas drove the demand for more detailed types of proteomic data. Now
researchers want information about where specific proteins are expressed, both
in terms of tissues and localization within the cell. Information relating
proteins to function require additional details of post- translational
modification, and studies of protein interactions have moved beyond just looking
at binary interactions to studies of protein complexes. For both genomics and proteomics, this
shift can be characterized as an interest in more contextual data. Enhanced
insight into biological context is essential for obtaining a better
understanding of how biology actually works, and thus there is now an emphasis
to move from genomic and proteomic snapshots to time series data of expression.
Such context is of particular value if biological studies are to be translated
into medical advances, because of the importance of being able to predict the
impact of potential treatments. The integration of genomic and proteomic data
with medical conditions, treatment and outcomes becomes another critical type of
contextual information. Christina Lingham, Beyond Genome: Thinking Globally,
Cambridge Healthtech
designer proteins:
Protein design is currently used for the
creation of new proteins with desirable traits. In our lab, we focus on the
synthesis of proteins with high essential amino acid content having potential
applications in animal nutrition. One of the limitations we face in this
endeavour is achieving stable proteins despite a highly biased amino acid
content. We report here the synthesis and characterisation of two mutants
derived from our MB-1 designer protein. Williams M, Gagnon MC, Doucet A,
Beauregard M, "Design
of high essential amino acid proteins: two design strategies for improving
protease resistance of the nutritious MB-1 protein" Journal of
Biotechnology 94(3): 245- 254, Apr. 11, 2002
proteins, Scripps http://mgl.scripps.edu/people/goodsell/pdb/pdb70/pdb70_1.html
Designer proteins can also refer to high- protein
nutritional supplements.
proteomes: Mass
spectrometry-based differential proteomics is a comprehensive analysis of
protein expression that involves comparing distinct proteomes, such as cells,
tissues or cell lines that are normal, diseased or treated. Mayo Clinic http://www.mayo.edu/research/core-resources/proteomics-core/mass-spectrometry-based-differential-proteomics
Differential proteomics makes qualitative and quantitative
comparisons of proteomes under different conditions. This knowledge enables us
to unravel the mysteries of biological processes. Genencor Proteome and Tools http://www.genencor.com/cms/connect/genencor/technology/protein_chemistry/proteomics/proteome_and_tools/proteome...
differential subproteomes: As defined
by relative solubilities, cellular location and narrow-range immobilised pH
gradients. . SJ Cordwell, AS Nouwens, NM Verrills, DJ Basseal, BJ Walsh,
Subproteomics based upon protein cellular location and relative solubilities in
conjunction with composite two-dimensional electrophoresis gels,
Electrophoresis, 21(6): 1094- 103, April 2000 Broader terms: subproteomes, subproteomics
docking: Three-
dimensional molecular structure is one of the
foundations of structure- based drug design. Often, data are available
for the shape of a protein and a drug separately, but not for the two together.
The program AutoDock was originally written in FORTRAN-77 in 1990 by David
S. Goodsell here in Arthur J. Olson's laboratory. It performs automated
docking of ligands (small molecules like a candidate drug) to their macromolecular
targets (usually proteins, sometimes DNA) Garrett B. Morris, Molecular
docking web, Scripps, Dec. 2000 http://www.scripps.edu/pub/olson-web/people/gmm/index.html
Wikipedia http://en.wikipedia.org/wiki/Docking_%28molecular%29
Narrower term: pharmacophore based docking
docking programs:
Programs for evaluating lead compounds against
target proteins; these programs are informed by structure data. Traditional ligand- docking programs - such as DOCK, developed by Irwin
Kuntz at the University of California at Berkeley; MacroModel, developed
by Clark Still at Columbia University; and GOLD from MSI (now part of
Pharmacopeia) - give information about potential ligands for a known protein structure.
These programs select molecules predicted to be highly complementary to
the receptor structure and can screen many of these ligands against the
protein. This type of virtual screening technology has already been incorporated into many
major pharmaceutical companies discovery programs and offers the ability
to screen many more compounds at once than the traditional laboratory- based
method. CHI Structural
proteomics report
docking studies:
Computational techniques for the exploration
of the possible binding modes of a substrate to a given receptor, enzyme
or other binding site. IUPAC Computational Related terms: drug design, QSAR
domain shuffling:
Creating new proteins by bringing domains together.
It is thought that this is a major way that new proteins have arisen during
evolution. Thus, mining of databases for homology by domains, rather than
by whole proteins (which are not as evolutionarily conserved), is important
in obtaining clues to functionality.
A protein
sequence can have more than one domain. Related term: multi- domain proteins.
energy function:
Computationally, a shape is assigned to a protein
sequence based on an empirical energy function. The lower the energy of
a given structure, the more likely it is to be the correct fold. The structure
prediction challenge is therefore divided into two: (1) The first challenge
is the creation of many plausible folds or a set of structures that will
include the native shape. The creation of the appropriate set depends on
existing databases (such as the Protein Data Bank) or on the design of
automated algorithms (using physical or statistical information) to generate
plausible folds. Once the set is available, a selection procedure is used
to ``fish'' out the correct fold. (2) The ``fishing'' of the plausible
native shapes critically depends on the quality of the energy function.
The value of the energy function must be the lowest for the native structure.
Opportunities in Molecular Biomedicine in the Era of
Teraflop Computing: March 3 & 4, 1999, Rockville, MD, NIH Resource
for Macromolecular Modeling and Bioinformatics Beckman Institute
for Advanced Science and Technology, University of Illinois at Urbana- Champaign
fold alignment:
A critical step in homology modeling,
because it provides the key structures for the model. If suitably
matched folds cannot be identified, a type of fold assignment known as
protein threading can be used.
fold recognition:
Methods of protein fold recognition attempt
to detect similarities between protein 3D structure that are not accompanied
by any significant sequence similarity. There are many approaches, but
the unifying theme is to try and find folds that are compatible with a
particular sequence. Unlike sequence- only comparison, these methods take
advantage of the extra information made available by 3D structure information. In effect,
the turn the protein folding problem on it's head: rather than predicting
how a sequence will fold, they predict how well a fold will fit a sequence.
Robert B. Russell, Guide to Structure Prediction "Fold recognition
methods and links" Sept. 1999 http://www.sbg.bio.ic.ac.uk/people/rob/CCP11BBS/foldrec.html
Related terms threading; Protein
structure. protein folding, protein folds
Methods for analyzing "foldedness" of expressed
proteins include NMR and circular dichroism
functional proteomics: As the emerging field
of proteomics continues to expand at an extremely rapid rate, the relative
quantification of proteins, targeted by their function, becomes its greatest
challenge. Complex analytical strategies have been designed that allow
comparative analysis of large proteomes, as well as in depth detection of the
core proteome or the interaction network of a given protein of interest.
Functional Proteomics, Methods in Molecular Biology 2008 http://www.springer.com/new+%26+forthcoming+titles+(default)/book/978-1-58829-971-0
Is yielding large databases of interacting proteins and extensive pathways.
Maps of these interactions are being scored and deciphered by novel high
throughput technologies. However, traditional methods of screening have not been
very successful in identifying protein- protein interaction inhibitors.
See also activity based protein
Hidden Markov Models HMM:
Searching a protein sequence database
for homologues is a powerful tool for discovering the structure and function
of a sequence. Amongst the algorithms and tools available for this task,
Hidden Markov model (HMM) - based search methods improve both the sensitivity
and selectivity of database searches by employing position- dependent scores
to characterize and build a model for an entire family of sequences. HMMs have been used to analyze proteins using two complementary strategies.
In the first, a sequence is used to a search a collection of protein families,
such as Pfam, to find which of the families it matches. In the second approach
an HMM for a family is used to search a primary sequence database to identify
additional members of the family. The latter approach has yielded insights
into protein involved in both normal and abnormal human pathology. Lawrence Berkeley Lab, US "Advanced
Computational Structural Genomics" http://cbcg.lbl.gov/ssi-csb/Meso.html
A widely used probabilistic model for data that are observed in a sequential
fashion (e.g., over time). A HMM makes two primary assumptions. The first
assumption is that the observed data arise from a mixture of K
probability distributions. The second assumption is that there is a discrete-
time Markov chain with K states, which is generating the observed
data by visiting the K distributions in Markov fashion. The
"hidden" aspect of the model arises from the fact that the state-
sequence is not directly observed. Instead, one must infer the state-
sequence from a sequence of observed data using the probability model. Although
the model is quite simple, it has been found to be very useful in a variety of
sequential modeling problems, most notably in SPEECH
RECOGNITION (Rabiner 1989) and more recently in other disciplines such as computational
biology (Krogh et al. 1994). MITECS Online MIT Encyclopedia of the
Cognitive Sciences http://cognet.mit.edu/MITECS/Entry/pearl.html
Related term: simulated annealing
homeomorphic superfamilies:
Protein families are clustered into "homeomorphic superfamilies". Sequences are homeomorphic if they can be aligned from
end- to- end. In practice, we allow the amino and carboxyl ends to be ragged and moderate internal length variations (represented as
gaps in the sequences). However, all members of the superfamily should have the same overall domain architecture, i.e., the same
domains in the same order (except for domains missing due to alternative splicing or very recent genetic events). It is assumed, although in most cases this has not been investigated in detail, that the molecules in a homeomorphic superfamily share a common evolutionary history since the acquisition of their constituent domains. Thus, it should be valid to construct an evolutionary tree from the members of a homeomorphic superfamily. If two groups of proteins with the same architecture are shown to have come to that structure independently, they are appropriately separated into two homeomorphic superfamilies.
PIR Classification Terminology, Georgetown Univ, revised 1998 http://pir.georgetown.edu/pirwww/aboutpir/doc/short_sf_def.html
Functional genomics
homology domains:
Many types of domains have been found in diverse proteins. In common use, the term "immunoglobulin superfamily" refers to the collection of all proteins that contain an
immunoglobulin- like domain. We call such a group a "homology domain superfamily". Any given protein sequence will be assigned to only one homeomorphic superfamily, but it may contain sequence segments belonging to several homology domain superfamilies.
PIR Classification Terminology, Georgetown Univ, revised 1998 http://pir.georgetown.edu/pirwww/aboutpir/doc/short_sf_def.html
homology model: A model of a protein, whose three-dimensional
structure is unknown, built from, e.g., the X-ray coordinate data of similar
proteins or using alignment techniques and homology arguments.
IUPAC Computational Related terms: Sequencing
homology modeling:
This procedure, also termed comparative modeling or
knowledge-based modeling, develops a three-dimensional model from a protein
sequence based on the structures of homologous proteins. ... Care must be used
in applying the term, "homology modeling." In fact, as noted above
some authors prefer alternative names for the procedure. One must recognize that
homology does not necessarily imply similarity. Homology has a precise
definition: having a common evolutionary origin [6,7]. Thus, homology is
a qualitative description of the nature of the relationship between two or more
things, and it cannot be partial. Either there is an evolutionary relationship
or there is not. An assertion of homology usually must remain an hypothesis.
Supporting data for a homologous relationship may include sequence or
three-dimensional similarities, the relationships between which can be described
in quantitative terms. David R. Bevan, Molecular Modeling of Proteins and
Nucleic Acids, Dept. of Biochemistry, Virginia Tech,
1997-2003 http://www.biochem.vt.edu/modeling/homology.html
A computational method for determining the
structure of a protein based on its similarity to known structures. The accuracy
of structures determined by homology modeling depends largely on the amount of
homology between the unknown and the known protein sequence. The most successful tool for prediction of
protein structure from sequence, but with significant room for improvement.
Related terms: structural homology; Sequencing
glossary sequence homology; Proteins glossary hypothetical
protein; In silico & Molecular
Modeling Compare with similarity
hypothetical proteins:
Many of the gene products of completely
sequenced organisms are hypothetical they cannot be related to any
previously characterized proteins and so are of completely unknown function.
..As each [completely sequenced] organisms genome is analyzed about one
third of the observed open reading frames (ORFs), although conserved among
several organisms, encode for hypothetical proteins that cannot be related
to other proteins of known function or structure. Understanding the physiological
function of the protein products of these so-called orphan genes has
emerged as a major challenge. E Eisenstein et al Biological function
made crystal clear annotation of hypothetical proteins via structural
genomics Current Opinion in Biotechnology 11(1): 25- 30 Feb. 2000
Searching for hypothetical proteins: theory and practice
based upon original data and literature. Lubec
G, Afjehi-Sadat L, Yang JW, John JP. Prog Neurobiol. 2005
Sep-Oct;77(1-2):90-127. Epub 2005 Nov 4.
All predicted protein sequences lacking any significant sequence similarity to characterised proteins are labeled
as hypothetical proteins'. The majority of these cases come from the genome
sequencing projects.
"SWISS- PROT" in Introduction to Molecular Biology Databases, R.
Apweiler, R. Lopez, B. Marx, 1999 http://www.ebi.ac.uk/panda/Publications/mbd1.html
in silico
Prediction of protein
structure and function. [Gareth W. Roberts and Jonathan Swinton "In Silico
Proteomics: Playing by the rules" Current Drug Discovery 5: Aug. 1, 2001
membrane proteins: http://en.wikipedia.org/wiki/Integral_membrane_protein
See also
under membrane proteins
Protein interaction maps have provided insight into the
relationships among the predicted proteins of model organisms for which a genome
sequence is available. These maps have been useful in generating potential
interaction networks, which have confirmed the existence of known
complexes and pathways and have suggested the existence of new complexes
and or crosstalk between previously unlinked pathways. However, the generation
of such maps is costly and labor intensive. Here, we investigate the extent to
which a protein interaction map generated in one species can be used to predict
interactions in another species. LR Matthews "Identification
of potential interaction networks using sequence- based searches for conserved
protein- protein interactions or "Interologs" Genome Research 11 (12):
2120- 2126, Dec. 2001
intrinsically disordered
proteins IDPs: Recent studies revealed that functional
proteins without unique 3-D structures are highly abundant in nature. These
intrinsically disordered proteins (IDPs) possess a number of crucial biological
functions that are complementary to functions of structured (ordered) proteins.
In any given organism, IDPs constitute a functionally broad and densely
populated unfoldome; i.e., a set of unstructured proteins in a proteome. Being
structurally and functionally very different from ordered proteins, IDPs require
special experimental and computational tools for their identification and
analyses. Intrinsically Disordered Proteins Unfoldome and Unfoldomics Gordon Research Conferences
2010 http://www.grc.org/programs.aspx?year=2010&program=intrinsic
location proteomics: Seeks
to provide automated, objective high-resolution descriptions of protein location
patterns within cells. Methods have been developed to group proteins into
statistically indistinguishable location patterns using automated analysis of
fluorescence microscope images. ... Preliminary work suggests the feasibility of
expressing each unique pattern as a generative model that can be incorporated
into comprehensive models of cell behaviour. RF Murphy, Location
proteomics: a systems approach to subcellular location, Biochem Society
Transactions, 33 (Pt 3): 535- 538, June 2005
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types,
peripheral and integral proteins. They include most
membrane- associated enzymes, antigenic proteins, transport proteins, and drug,
hormone, and lectin receptors. MeSH, 1977 Narrower term: Drug
& disease targets G-protein-coupled receptors GPCRs;
Related term: Microarray
categories membrane microarrays membrane transport
proteins: Membrane proteins whose primary function is to
facilitate the transport of molecules across a biological membrane. Included in
this broad category are proteins involved in active transport (BIOLOGICAL
TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS. MeSH 2002
January 21-22, 2015 San Diego, CA Program | Register | Download
glossary of membrane transport proteins,
IUBMB International Union of Biochemistry and Molecular Biology, 2002, 13
definitions http://www.chem.qmul.ac.uk/iubmb/mtp/intro.html#glossary
Are there any
transport proteins which are not membrane proteins? Broader term:
carrier proteins
Membrane proteins comprise the largest set
of proteins to resist high-throughput structural genomics efforts. One of the
major impediments to the analysis of membrane proteins is the lack of generic
and effective expression systems. The aims of the membrane protein platform are
to develop the methodologies to perform high-throughput cloning, expression,
purification and crystallization of membrane proteins. To date, we have
purified over 30 targets to homogeneity. This represents ~10% of the total
number of genes cloned (compared to an average of 40% for similar efforts with
soluble proteins). The proteins we have purified include several active
prokaryotic and eukaryotic rhomboid proteases and human G protein-coupled
receptors (GPCRs). "Membrane Proteomics", A Edwards Labs, Univ.
of Toronto, Canada, 2004 http://www.utoronto.ca/AlEdwardsLab/membrane_proteomics_index.html
Membrane proteins
perform some of the most important functions in the cell, including the
regulation of cell signaling through surface receptors, cell-cell interactions,
and the intracellular compartmentalization of organelles. Recent developments in
proteomic strategies have focused on the inclusion of membrane proteins in
high-throughput analyses. While slow and steady progress continues to be made in
gel-based technologies, significant advances have been reported in non-gel
shotgun methods using liquid chromatography coupled to mass spectrometry
(LC/MS). Wu CC, Yates John R, The
application of mass spectrometry to membrane proteomics Nature Biotechnology
21(3): 262- 267, March 2003
Related terms: membrane proteins, membranomics
Monte Carlo technique:
A simulation procedure consisting of randomly
sampling the conformational space of a molecule. IUPAC Computational Broader
term: simulation
ontologies - proteomics:
principal aim of post- genomic biology is elucidating the structures, functions
and biochemical properties of all gene products in a genome. However, to
adequately comprehend such a large amount of information we need new
descriptions of proteins that scale to the genomic level. In short, we need a
unified ontology for proteomics. Much progress has been made towards this end,
including a variety of approaches to systematic structural and functional
classification and initial work towards developing standardized, unified
descriptions for protein properties. In relation to function, there is a
particularly great diversity of approaches, involving placing a protein in
structured hierarchies or more- generalized networks and a recent approach based
on circumscribing a protein's function through systematic enumeration of
molecular interactions. N Lan, GT Montelione, M. Gerstein, Ontologies for
proteomics: towards a systematic definition of structure and function that
scales to the genome level, Current Opinion in Chemical Biology 7(1): 44- 54,
Feb. 2003
ORFeome: Omes & omics glossary
peptide mapping, peptide maps: Maps, genomic & genetic
peptidomics: -Omes &
-omics glossary
phylogenetic profiles: Phylogenomics glossary
Can be used to hypothesize protein function.
those proteins that do not have significant sequence identity(>10%) with
other known proteins.
Bioinformatics.Org general forum
Characterization of post- translational modifications in
proteins is one of the major tasks that is to be accomplished in the post-
genomic era. Phosphorylation is a key reversible modification that regulates
enzymatic activity, subcellular localization, complex formation and degradation
of proteins. DE Kalume et. al, Tackling
the phosphoproteome: tools and strategies, Current Opinion in Chemical
Biology 7(1): 64- 69, Feb. 2003
Ahn NG, Resing KA (2001) Toward
the phosphoproteome. Nature Biotechnology 19:317- 19318
Developments in the field of phosphoproteomics have been fueled by the need
simultaneously to monitor many different phosphoproteins within the signaling
networks that coordinate responses to changes in the cellular environment. Marc
Mumby, Deirdre Brekken, Phosphoproteomics: new insights into cellular signaling,
Genome Biology 2005,
6:230 doi:10.1186/gb-2005-6-9-230
post- translational modification identification:
ExPASy Proteomics
Tools http://www.expasy.ch/tools/#ptm
list a number of tools for prediction of post- translational modification, as do
other websites. Identification of these modifications may provide important
structural- functional information.
predicted proteins:
ORFs with no similarity to other sequence were named predicted
proteins. MIT, Broad Institute, Methanosarcina project
information, 2004 http://www.broad.mit.edu/annotation/microbes/methanosarcina/background.html
The search for predictive biomarkers of disease from high-throughput mass
spectrometry (MS) data requires a complex analysis path. Preprocessing and
machine-learning modules are pipelined, starting from raw spectra, to set up a
predictive classifier based on a shortlist of candidate features. As a
machine-learning problem, proteomic profiling on MS data needs caution like the
microarray case. The risk of overfitting and of selection bias effects is
pervasive: not only potential features easily outnumber samples by 103
times, but it is easy to neglect information-leakage effects during
preprocessing from spectra to peaks. Machine learning methods for predictive proteomics, Annalissa Barla et. Al
Briefings in Bioinformatics (2008) 9 (2): 119-128. doi: 10.1093/bib/bbn008
probable protein: See under putative proteins
probable protein (similarity):
When a protein exhibits extensive sequence similarity to a characterised protein
and/ or has the same conserved regions then the label probable' is used in the DE line.
"SWISS- PROT" in Introduction to Molecular Biology Databases, R.
Apweiler, R. Lopez, B. Marx, 1999 http://www.ebi.ac.uk/panda/Publications/mbd1.html
Related term: Protein categories putative protein
protein analysis
sequencing: A process that includes the determination of AMINO ACID SEQUENCE
of a protein (or peptide, oligopeptide or peptide fragment) and the information
analysis of the sequence. MeSH 2000
protein array
Ligand-binding assays that
measure protein- protein, protein- small molecule or protein- nucleic acid
interactions using a very large set of capturing molecules, i.e., those attached
separately on the solid support, to measure the presence or interaction of
target molecules in the sample. MeSH 2003
protein bioinformatics:
Tools for Protein Informatics sequence and structure comparison
multiple alignments phylogenetic tree construction
composition/pI/mass analysis motif/pattern identification 2° structure
prediction/threading TMD prediction/hydrophobicity analysis homology
modeling visualization A Very very very short introduction to
protein bioinformatics, Patricia
Babbitt 2003 http://pga.lbl.gov/Workshop/May2003/lectures/Babbitt.pdf
See also Proteomics
informatics Is there a difference?
protein databases:
Protein location can be determined by such genome-
wide techniques as green fluorescent protein (GFP) tagging, and protein-
protein interactions can be determined by affinity chromatography,
immunoprecipitation and yeast two- hybrid experiments. Databases resulting from
these methods are beginning to emerge, but they are of uncertain accuracy.
Defining the Mandate of Proteomics in the Post- Genomics Era, Board on
International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
Dr. Stanley Fields, Professor of Genetics and
Medicine at the Univ. of Washington and developer of the yeast two hybrid system
writes that protein databases "will need to become much more sophisticated
if they are to help scientists make sense of the staggering number of experimental
measurements that will soon emerge. ... protein
data will need to be integrated with results from expression profiling, genome-
wide mutation or antisense analyses, and polymorphism detection.
As proteomic data accumulate, we will become better at triangulating from
multiple disparate bits of information to gain a bearing on what a protein
does in the cell. S. Fields "Proteomics in Genomeland" Science
291: 1221-1224 Feb. 16, 2001 Related terms: protein identification, protein localization; Expression
glossary expression profiling
Protein databases Databases
& software directory
protein dynamics: Certain parts of a particular protein will
be rigid, but others may be flexible and change their shape, even when
bound. ... NMR has the unique ability to characterize protein fluctuations
quantitatively, much more so than crystallography can. Understanding the function of a protein is fundamental for gaining insight
into many biological processes. Proteins are stable mechanical constructs
that allow certain internal motions to enable their biological function.
Structural properties of a protein can be obtained with X-ray
crystallography or NMR acquisition techniques. Molecular dynamics
(MD) simulations at pico/ nano- second time scales output one or more
trajectory files which describe the coordinates of each individual atom
over time. The main problem with animating these trajectories is one of
temporal scale. Taking large time steps will destroy the impression of
smooth motion, while small time steps will result in the camouflage of
interesting motions. [Henk Huitema, Robert van Liere " Interactive Visualization
of Protein Dynamics" ERCIM [European Research Consortium for Computers
and Informatics] News No. 44 - January 2001] http://www.ercim.org/publication/Ercim_News/enw44/van_liere.html
protein expression mapping: Maps, genetic
& genomic
protein expression profiling: Expression
protein folding problem: Protein
structures See also protein structure
function: The focus of the group is the understanding
of protein function and evolution using genomic, structural and proteomic data.
Central to this question is the concept of the domain: a structurally conserved,
genetically mobile unit. When viewed at the three-dimensional level of protein
structure, a domain is a compact arrangement of secondary structures connected
by linker polypeptides. It usually folds independently and possesses a
relatively hydrophobic core. The importance of domains is that they cannot be divided
into smaller units they represent a fundamental building block that can be used
to understand the evolution and function of proteins... The advent of
complete genomic sequences, including more and more eukaryotes, is leading to a
fundamental change in protein domain analysis. Having characterised most of the
domain families and having developed tools to predict them, we can now start to
analyse their function and evolution on a higher level. Protein
Function Analysis Group, Max Planck Institute for Molecular Genetics, Germany
Function is not a fixed property for many, if not
most proteins. There are many ways that gene products can be altered to elicit
modified or completely new functions. For example there are exist - alternative
splicing - which may affect as many as ¼ or more of the genes in a higher
eukaryote and can alter biochemical function either drastically or subtly,
producing truncated proteins and proteins with different compositions - post-
translational modification, such as phosphorylation and glycosidation
(which can occur on numerous sites on the same protein) - pre-enzymes made for
secretion and pro- enzymes that are activated by cleavage - acylation and
ubiquitination - non- enzymatic modifications like oxidation, so a given protein
exists in the cell in different oxidized states. Defining the Mandate of
Proteomics in the Post- Genomics Era, Board on International Scientific
Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
More systematic attempts have been made to place
proteins within a hierarchy of standard functional categories or to connect them
in overlapping networks of varying types of associations. These networks
can obviously include protein- protein interactions ... More broadly, they can
include pathways, regulatory systems and signaling cascades... Perhaps, in the
future, the systematic combination of networks may provide for a truly rigorous
definition of protein function. Mark Gerstein, et. al "Integrating
Interactomes" Science 295 (5553): 284, Jan. 2002
A biologically useful definition of the function of a protein requires a description at several different levels. To the biochemist, function means the biochemical role of an individual protein: if it is an
enzyme, function refers to the reaction catalyzed; if it is a signaling protein, function refers to the interactions that the protein makes. To the geneticist or cell biologist, function includes these roles but will also encompass the cellular roles of the protein, such as the
phenotype of its deletion, the pathway in which it operates, among others. A physiologist or developmental biologist may have an even broader view of function, including tissue specificity and
expression during the life cycle of the organism.
Gregory A Petsko, Dagmar Ringe "Overview: The Structural Basis of Protein
Function" from Chapter 2 of Protein Structure and Function: New Science
Press, 1991-2001
In the expanded view of protein function, a
protein is defined as an element in the network of its interactions. Various
terms have been coined for this expanded notion of function, such as contextual
function or cellular function
Whatever the term, the idea is that
each protein in living matter functions as part of an extended web of interacting
Often it is possible to understand the cellular functions of
uncharacterized proteins through their linkages to characterized proteins.
In broader terms, the networks of linkages offer a new view of the meaning
of protein function, and in time should offer a deepened understanding
of the function of cells. David Eisenberg et al "Protein function in the post-
genomic era" Nature 405: 823- 826, 15 June 2000
The principal problem facing the post- genome era.
Walter Blackstock & Malcolm Weir "Proteomics" Trends in Biotechnology: 121-134 Mar
Related terms: Protein
categories interaction proteomics; Functional
genomics glossary gene function, Gene OntologyTM
; Maps
protein identification:
The analytical method used most commonly to
visualize and identify large numbers of proteins is 2D-gel electrophoresis.
One can theoretically visualize changes in protein production, both
qualitatively and quantitatively, from two individual samples (e.g., a
control preparation and a treated preparation). Furthermore, one can potentially
accomplish protein identification by "picking" proteins from the 2D-
gel and subjecting the highly purified protein to MALDI- TOF mass
spectrometry. "High - Throughput Genomics, CHI Genome Link
14.1 http://www.chidb.com/newsarticles/issue14_1.asp
Related term: protein databases
protein informatics:
The Protein Informatics Group currently consists of a collaboration between
researchers at the Oak Ridge National Laboratory, the University of Missouri,
and the University of Georgia. Our common interests are in development of
computational tools for solving problems from molecular biology. Our work ranges
from construction of mathematical/statistical models to development of
algorithms to code implementation on various platforms to applications of
computational tools to solve various bio-data analysis problems. Protein Informatics Group, Computational Biology, Oak Ridge
National Lab, US http://compbio.ornl.gov/structure/
biological research has become an essential component of biological research. The great quantity
and diversity of the data being generated by different technologies is daunting,
and impossible to organize or oversee without computational assistance. In
functional genomics, a great deal of effort has been devoted to developing
community- based standards for reporting gene expression data to allow others to
replicate experiments. The same will need to be done for proteomics to validate
across the different technologies. Perhaps never before has a bioinformatics
problem of this magnitude been approached. Without effective and integrated
databases to store and retrieve these data and advanced computational methods
such as pattern recognition and other machine learning approaches to analyze and
interpret them, the full implications of these data will not be realized.
Defining the Mandate of Proteomics in the Post- Genomics Era, Board on
International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
Although mining of protein
structure homology data is a relatively small field now, it is likely to
experience dramatic growth and to become pivotal in the ultimate exploitation of
genomic data and tools. Related
terms: proteoinformatics; Algorithms glossary;
protein bioinformatics; In Silico & molecular modeling
protein interactions:
Narrower terms: protein DNA interactions, protein protein interactions, protein RNA
interactions Related terms: annotation- proteins, binary
interaction, interaction proteomics, protein networks; -Omes
& -omics glossary interactome
protein interaction mapping: Maps genomic
& genetic
protein linkage maps: Maps genomic &
protein & mRNA data:
Although the relationship between
mRNA and
protein levels is vague for individual genes, some of the statistics for broad
categories of protein properties are much more robust... In contrast to the
differences between mRNA and protein data for individual genes, the broad
categories show that the transcriptome and translatome populations are
remarkably similar; both contain roughly the same proportions of secondary
structure and functional categories. Moreover, this contrasts the difference
with the genome, which appears to have a distinctly different composition of
functional categories. This illustrates that we get a more consistent picture
when we average across the population, i.e. there is broad similarity between
the characteristics of highly expressed mRNA and highly abundant proteins.
Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of
Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
Related terms:
Expression glossary; Genomics
glossary genome data; functional
genomics data Omes & omics
transcriptome, translatome
protein networks:
The individual steps in signal
transduction pathways involve protein interactions with target molecules that
may be other proteins, small molecules or DNA. Identifying all of the proteins
that take part in a given class of interactions, on a genome-wide scale, remains
an extremely challenging task. We propose to apply mRNA display (1,
2) technology to this problem, with the goal of developing
databases of protein-ligand interactions that will add value to the existing and
growing sequence databases. PI Jack Szostak, Definition of Protein Networks
using mRNA display, ParaBioSYs, MGH, HMS, BU http://pga.mgh.harvard.edu/Parabiosys/projects/protein_networks_rna_display.php
protein sequence:
A process that includes the determination of an amino acid
sequence of a protein (or peptide, oligopeptide or peptide fragment) and the
information analysis of the sequence. MeSH, 2002 See
also amino acid sequence.
protein sequence space: [J.] Maynard-Smith's (1970. Natural Selection and the concept of a protein space. Nature 225: 563- 564) concept of a "protein
sequence space" in which each site in an alignment is represented on its own axis and the number
of axes required to represent all conceivable variants for a protein is equal to the number of sites
in its sequence. Each sequence occupies a unique point in this space; variants differing at one site
are adjacent (Hamming) neighbours. The collection of all viable sequence variants for a
particular protein forms a localized interconnected `neighbourhood' of points within the space.
This representation has proved conceptually intuitive and analytically powerful
In protein sequence space, constraints are reflected in the multidimensional shape of the
cluster of points that make up the "neighbourhood" of variants viable for a specific protein. The
boundary defining the edge of this neighbourhood is characteristic of the protein's function and
can be thought of as its functional "signature". Gavin JP Naylor,
"Measuring Shifts In Function and Evolutionary Opportunity Using
Variability Profiles: A Case Study of the Globins" also Journal of
Molecular Evolution 51 (3): 223-233 Sept. 2000 http://bioinfo.mbb.yale.edu/e-print/protspace-jme/text.pdf
protein sorting signals:
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
MeSH, 2001
Spotlight, Swiss-Prot http://au.expasy.org/spotlight/
One month, one protein
Protein Structure Initiative:
Aims at determination of the 3D
structure of all proteins. This aim can be achieved in four steps: Organize
known protein sequences into families; Select family representatives
as targets; Solve the 3D structure of targets by X-ray crystallography
or NMR spectroscopy; Build models for other proteins by homology to solved
3D structures. http://www.structuralgenomics.org/
Protein Structure
Initiative NIGMS http://www.nigms.nih.gov/funding/psi.html
protein structure prediction:
Methods for
protein structure prediction have matured to the point where models produced by
prediction algorithms can be used to understand and test hypotheses about
biological function. The goal of this community wide effort is to provide
structural and functional insights into biologically important proteins,
particularly those that are intractable to experimental structural
determination. Ten Most Wanted, Critical Assessment of Techniques for Protein
Structure Prediction, CASP, Lawrence Livermore National Lab, US http://predictioncenter.llnl.gov/
Protein 3D structures are encoded
by a linear sequence of amino acid residues. To predict 3D structure from
sequence is a task challenging enough to have occupied a generation of
researchers. Have we finally succeeded? The bad news is: we still cannot
predict structure for any sequence. The good news is: we have come closer,
and growing databases facilitate the task. A solution of the structure
prediction problem would supposedly change experimental molecular biology
more than any other theoretical method. We may witness such a break- through
in the near future. However, the lessons from the Asilomar prediction contests
were that we may need a common frame- work to co- ordinate the efforts of
the researchers in the field. "Neural networks for protein structure prediction:
hype or hit? Burkhard Rost, Dec. 1999 http://www.embl.de/~rost/Papers/pre1999_tics/paper.html
Involves primary sequence alignment,
secondary and tertiary structure prediction and homology modelling.
Narrower term: ab initio
protein structure prediction
protein taxonomy:
Protein Taxonomy Based on Secondary Structure T. Przytycka, R. Aurora, GD Rose, Nature Structural Biology 6
(7): 1999.
protein threading: See
proteome informatics:
Peer Bork and David Eisenberg, "Genome and
proteome informatics" Current Opinion in Structural Biology 10 (3):
341-342, 2000
Proteome Informatics group
is part of the Swiss
Institute of Bioinformatics (SIB). It is in charge of research and
development in the fields of bioinformatics, molecular imaging
and the use of Internet for biomedical applications. Current Projects and
People, ExPASy, Swiss Institute of Bioinformatics http://au.expasy.org/people/pig/
proteome map: Maps, genomic & genetic
proteome mining:
present the development and application of a new machine-learning approach to
exhaustively and reliably identify major histocompatibility complex class I
(MHC-I) ligands among all 208 octapeptides and in genome-derived proteomes of Mus musculus, influenza A H3N8, and vesicular stomatitis virus (VSV).
Exhaustive Proteome Mining
for Functional MHC-I Ligands ACS
Chem. Biol., 2013, 8 (9),
pp 18761881 DOI: 10.1021/cb400252t
Related term: proteome database mining
proteomic analysis:
Systematic and
quantitative analysis of the properties that define protein activity and
functions within a defined context, essential for biology and medicine. Ruedi
Aebersold quoted in Defining the Mandate of Proteomics in the Post- Genomics
Era, National Academies Press, 2002 http://www.nap.edu/books/NI000479/html/R1.html
systematic analysis of proteins for their identify quantity and function. J Peng
and Steven Gygi, Proteomics: the move to mixtures, Journal of Mass Spectrometry
35: 1083- 1091, 2001
Standards Initiative PSI:
The HUPO Proteomics Standards Initiative (PSI)
defines community standards for data representation in proteomics to facilitate
data comparison, exchange and verification. Proteomic Standards Initiative,
HUPO http://www.psidev.info/
putative proteins:
Some similarity to one or more existing entries It is in this category that
the adjective "putative" comes into play. For these cases, again there
is no experimental proof that the protein exists and there is only limited
evidence to point the protein to a particular family. Again, we have no fixed
rules on what is "limited" and what isn't. It is a judgment that we
make based on which family it is and which, if any, areas are conserved. A
primer on UniProtKB/Swiss-Prot annotation Name: ANNBIOCH.TXT Release: 54.0 of
24-Jul-2007 http://www.expasy.ch/cgi-bin/lists?annbioch.txt
The label putative' is used in the DE [descriptor] line of proteins that exhibit limited sequence similarity to characterised proteins. These proteins often have a conserved site e.g. ATP-binding site but no other significant similarity to a characterised protein. It is most frequently used for sequences from genome projects.
The assignment of the labels probable' and putative' is dependent primarily on the results of
sequence similarity searches against
SWISS- PROT. It is important to point out here that no specific cut- off point is used to assign a protein as putative' or
probable'. "SWISS- PROT" in Introduction to Molecular
Biology Databases, R. Apweiler, R. Lopez, B. Marx, 1999 http://www.ebi.ac.uk/panda/Publications/mbd1.html Related term probable protein (similarity)
quantitation - proteins:
It is likely that in the
near future, researchers will continue to use comprehensive gene arrays at the
start of their work, to generate hypotheses and narrow their research questions.
Then, they might delve deeper into these questions by using non-array- based
gene expression studies (to get better quantitation and true relative
expression) or go to a focused protein array that covers most of proteins that
are indicated based on the gene array experiments. "Proteomewide
chips - not so fast" CHI's GenomeLInk 21.2 http://www.chidb.com/newsarticles/issue21_2.asp
regulatory homology:
Quantitative analysis of protein expression data
obtained by high - throughput methods has led us to define the concept of
"regulatory homology" and use it to begin to elucidate the basic
structure of gene expression control in vivo. N. Leigh Anderson, Norman
G. Anderson "Proteome and proteomics; New technologies, new concepts, and
new words" Electrophoresis 19(11):1853-61 August 1998
regulatory proteins: A detailed understanding
of the interplay between regulating proteins and DNA targets is required to
interpret transcriptomic data and to model the dynamics of genetic networks. Two
key problems in this respect are the control of protein traffic on DNA and the
combined effects of several regulating proteins operating on the same target
gene. [International Workshop on Regulatory Proteins Interplay and Traffic
on DNA, July 12-13, 2002, Evry, France http://www.lami.univ-evry.fr/~epigenese/Ecoles/Autrans/workshop.html
reverse proteomics:
In reverse proteomics, the starting point is the
DNA sequence of the genome of an organism. First, the transcriptome (complete
set of transcripts) and proteome (complete set of proteins) are predicted in
silico and subsequently this information is used to generate reagents for
their analysis. Marc Vidal, AJ Walhout, "Protein Interaction Maps for Model Organisms" Nature
Reviews Molecular Cell Biology 2; 55- 63, Jan. 2001 http://www.nature.com/nrm/journal/v2/n1/slideshow/nrm0101_055a_F2.html
Compounds can be tested to see if they
can disrupt protein - protein interactions - a strategy that may be extremely
useful for the development of new drugs. [Wellcome Trust, UK "The Human
Genome Functional Genomics"]
RNA structural genomics:
The systematic determination of all
macromolecular structures represented in a genome, is focused at present
exclusively on proteins. It is clear, however, that RNA molecules play a variety
of significant roles in cells, including protein synthesis and targeting,
many forms of RNA processing and splicing, RNA editing and modification,
and chromosome end maintenance. To comprehensively understand the biology of a cell, it will ultimately be necessary to know the identity of all encoded RNAs,
the molecules with which they interact and the molecular structures of these
complexes. This report focuses on the feasibility of structural genomics of RNA,
approaches to determining RNA structures and the potential usefulness of an RNA
structural database for both predicting folds and deciphering biological
functions of RNA molecules. [Jennifer A. Doudna "Structural Genomics of
RNA" Nature Structural Biology 7 (11) supp: 954-956 (Nov. 2000]
Rosetta stone method: A way of looking at the correlation of
domains across species. Some proteins have homologs that are fused
in other species, yielding clues as to the proteins with which they might
interact. In addition, proteins that have been identified in particular
complexes and pathways hint at the location and function of their homologs
in other species. S. Spengler Bioinformatics in the information age
Science 287 (5451): 221- 223 Feb. 18, 2000 Related term: Phylogenomics glossary phylogenetic profiles
sequence homology, amino acid
The degree of similarity between sequences of amino acids. This information is useful for the understanding of genetic relatedness of certain species.
MeSH, 1993
signal transduction: Metabolic
engineering glossary
Quantity that indicates for example the percentage
identical amino acids between two sequences. Similarity is an observed quantity,
that might be for example be expressed in percent of residues that are similar
between two aligned sequences. Similarity is a bad measure, because it is
subjective. The author of the software decides whether Gln and Asp are similar
or not. The percentage identity is a much better measure. There
is an important difference between similarity and homology. Similarity is a
value between 0.0 and 1.0, or between 0 and 100%. On the other hand, there are
no degrees of homology. The sequences are either homologous or not. Center for Molecular and Biomolecular Informatics,
Dictionary, Univ. of Nijmegen,
Netherlands, 2001 http://www.cmbi.kun.nl/gvteach/dictionary.shtml
structural bioinformatics:
Involves the process of determining
a protein's three- dimensional structure using comparative primary sequence
secondary and tertiary structure prediction methods, homology modeling,
and crystallographic diffraction pattern analyses. Currently, there is
no reliable de novo predictive method for protein 3D- structure determination.
Over the past half- century, protein structure has been determined by purifying
a protein, crystallizing it, then bombarding it with X-rays. The X-ray
diffraction pattern from the bombardment is recorded electronically and
analyzed using software that creates a rough draft of the 3D structure.
Biological scientists and crystallographers then tweak and manipulate the
rough draft considerably. The resulting spatial coordinate
file can be examined using modeling- structure software to study the gross
and subtle features of the protein's structure. Christopher Smith "Bioinformatics,
Genomics, and Proteomics" Scientist 14[23]:26, Nov. 27, 2000 http://the-scientist.com/yr2000/nov/profile_001127.html Related terms Algorithms,
In silico & Molecular
Structural Biology Industrial Platform:
Fifteen companies, including
representatives of some of Europe's largest pharmaceutical industries,
have formed the Structural Biology Industrial Platform to work with each
other, the European Commission and Research Centres in Europe to promote
structural biology research, training and development. http://www.sbip.org/
structural genomics:
Focuses on the physical aspects of the genome through the
construction and comparison of gene maps and sequences, as well as gene
discovery, localization, and characterization. Brush up on your 'omics, Chemical
& Engineering News, 81(49): 20, Dec. 2003 http://pubs.acs.org/cen/coverstory/8149/8149genomics1.html
The fast-developing
fields of structural and functional genomics -- studies of proteins encoded by
the entire genome -- are being brought to bear on the problem of understanding
the root of many cancers. A protein's structure can tell researchers much about
its function, information that ultimately is needed to understand a protein's
link to cancer. By determining the detailed, three- dimensional structure of
proteins, researchers are better able to understand how each protein functions
normally and how faulty protein structures can cause disease. David Brand,
MacCHESS moves into cancer research through structural genomics, Cornell,
2001 http://www.news.cornell.edu/Chronicle/01/2.22.01/MacCHESS.html
Involves quickly determining the 3D structures of large numbers of
(or other complex biological molecules, such as nucleic acids), ultimately
accounting for an organisms entire proteome. Footnote: As traditionally
defined, the term structural genomics referred to the use of sequencing
and mapping technologies, with bioinformatic support, to develop complete
genome maps (genetic, physical, and transcript maps) and to elucidate genomic
sequences for different organisms, particularly humans. Now, however, the
term is increasingly used to refer to high- throughput methods for determining
protein structures
Many of the criticisms leveled at the Human Genome Project in
the mid- 1980s have been redirected toward structural genomics. Unlike high-
throughput genome sequencing, it is not a simple matter to decide
when a structural genomics effort has reached completion. SK Burley et
al Structural genomics: beyond the Human Genome Project Nature Genetics
23: 151 Oct. 1999 Related term: structural proteomics
A good
explanation of structural genomics Joint
Center for Structural Genomics http://www.jcsg.org/help/robohelp/Definitions/Structural_Genomics.htm
Human Proteome/Structural Genomics Pilot Project, Brookhaven National
Laboratory, US http://www.proteome.bnl.gov/
A pilot project to examine the feasibility of high-throughput
determination of 3-dimensional structures of proteins by x-ray crystallography,
starting from genome sequences.
Human Proteomics Initiative, Swiss Institute of Bioinformatics, European
Bioinformatics Institute http://us.expasy.org/sprot/hpi/
A major project to annotate all known human sequences
according to the quality standards of Swiss- Prot. This means providing, for
each known protein, a wealth of information that include the description of its
function, its domain structure, subcellular location, post- translational
modifications, variants, similarities to other proteins, etc.
Structural Genomics Initiative,
NIGMS, US http://www.nigms.nih.gov/funding/psi.html
Structural genomics databases Databases & software
structural homology: Identify
3D structures of proteins or domains in the same family as a sequence of
Related terms: homology Functional
genomics glossary homology modeling Molecular
modeling glossary
structural homology
The degree of 3-dimensional shape similarity between proteins. It
can be an indication of distant AMINO
ACID SEQUENCE HOMOLOGY and used for rational DRUG
DESIGN. MeSH 2003
structural proteomics:
is focused on the
determination of three-dimensional (3D) structures of annotated and un-annotated
emerged from the simultaneous developments of rapid and parallel
methodologies in gene cloning, protein purification, and 3D structure
determination and recent results have demonstrated the feasibility and
importance of this approach for functional annotation. The classic work by
Zarembinski et al. (1998, PNAS, 95: 15189-15193) represents one possible outcome
of the structural analysis of an unknown protein, in which a protein-bound
ligand or cofactor was discovered. Such information is the most useful for
functional annotation because it identifies the nature of the ligand, the
ligand-binding site and the disposition of catalytic residues, from which a
catalytic mechanism can be postulated. Other sources of structure-derived
information come by identifying structural homologues in databases or local
structural motifs or putative catalytic sites. Our strategy involves the use of
X-ray crystallography and NMR spectroscopy to determine the structures of
hypothetical proteins. Yeast Integrative Biology Project
Canada funded, University of Toronto http://yeastgenomics.ca/structure
Sometimes referred to as structural genomics, this
discipline involves determining the 3D structures of large numbers of proteins,
ultimately accounting for an organism's entire proteome. It adds critical
information in at least two points in the drug discovery pathway: (1) target
identification, or selecting a pathway in which a drug might function, and (2)
medicinal chemistry, or the actual design of compounds to modulate this pathway. A high-throughput, system wide means of determining gene
function. It
typically involves using high- throughput X-ray diffraction methods to determine
the structure of proteins encoded by at least one member of each gene
family in the genome. This approach is coupled with the use of bioinformatics
as a tool in structural proteomics and computational modeling
to determine structures of other proteins in the same family. Conversely, an
important goal of structural proteomics is the creation of databases of
structures. When asked to identify bottlenecks in the structural proteomics field,
several academic and industry scientists pointed to the need for faster and more
reliable protein production and purification strategies, rather than stronger
beams at the X-ray crystallization step.
structure based design:
A design
strategy for new chemical entities based on the three- dimensional (3D) structure of the target obtained by X-ray or nuclear
magnetic resonance (NMR) studies, or from protein homology models. IUPAC
structure- based
drug design: Structure-based drug design took
nearly two decades of multiple, parallel technological improvements to arrive at
its current mainstream position in medicinal chemistry. Developments in computer
graphics, high-power radiation sources, computational processing power,
refinement protocols, virtual screening and crystallography were all necessary
to create the environment for rapid, iterative structure-based drug discovery.
Given the crisis facing the pharmaceutical industry in the
translation of early stage drug discovery results, a different set of tools,
concerned with algorithms and methods for predicting the biological profiles,
will need to be refined.
Structure-Based Drug Design May 21-22,
2014 Boston, MA Program | Register |
structure from sequence:
See protein structure prediction,
structural homology
structure prediction problem:
The protein secondary structure
prediction problem has become a classic, challenging problem for the artificial-
intelligence and machine learning community. Virtually every conceivable
computational technique in these fields (e.g., information theory [6, 12, 13], artificial
neural networks [15, 20, 22], cascaded networks [18, 19, 27], hybrid systems
[28], nearest neighbor methods [21], hidden markov chains [4], machine
learning [17, 25], mutual information [26]) has been applied in the context of
protein structure prediction. The reason for this attention is well- founded and
clear: If protein structure, even secondary structure, can be accurately
predicted from the now abundantly available gene
and protein sequences, such
sequences become immensely more valuable for the understanding of drug-
design, the genetic basis of disease, the role of protein
structure in its enzymatic, structural, and signal transduction
functions, and basic physiology from molecular to cellular, to fully systemic
levels. In short, the solution of the protein structure prediction problem (and
the related protein folding problem) will bring on the second phase of
the revolution. Peter Munson et. al "Protein Secondary Structure
Prediction, NIH, 1994 http://abs.cit.nih.gov/reprints/text3.html
SWISS- PROT: Databases &
software directory
In this approach, a target sequence is threaded
through a library of 3D folds to try to find a match. This method
is used when no sequence is clearly related to the target sequence.
virtual genomes:
A distributed computing project to use protein design
to generate new "virtual genomes." Our project, Genome@home,
studies real genomes and proteins directly, by designing new sequences for
existing 3-D protein structures, which come from real genomes. The protein
structure files that are sent out as work contain the Cartesian atomic
coordinates of a protein. This data was obtained experimentally through X-ray
crystallography or NMR techniques. Note that this was not done by us;
thousands of scientists have spent decades compiling this data, which is
generously made freely available to the public. By designing new sequences that
could form these specific protein structures, we're setting the stage to attack
a number of significant contemporary issues in structural biology, genetics, and
medicine. Vijay Pande, Pande Group Projects, Stanford Univ. US http://www.stanford.edu/group/pandegroup/projects.html#design
whole proteom
Proteome analysis has become indispensable and complementary to genomic analysis. With access to whole genome sequences from various organisms and with the imminent completion of many more, the
SWISS- PROT group at EBI has developed a research- oriented initiative that utilises many of the existing resources and provides comparative analysis of the
predicted protein coding sequences of all complete genomes. Rolf Apweiler
"Whole Proteome Analysis: The role of InterPro and CluSTr" Plant &
Animal Genome IX, San Diego CA Jan. 13-17, 2001 http://www.intl-pag.org/pag/9/abstracts/W22_01.html
whole proteome interaction mining:
major post- genomic scientific and technological pursuit is to describe the
functions performed by the proteins encoded by the genome. One strategy is to
first identify the protein- protein interactions in a proteome, then determine
pathways and overall structure relating these interactions, and finally to
statistically infer functional roles of individual proteins. Although huge
amounts of genomic data are at hand, current experimental protein interaction
assays must overcome technical problems to scale- up for high- throughput
analysis. In the meantime, bioinformatics approaches may help bridge the
information gap required for inference of protein function. JR Bock, DA Gough, Whole-
proteome interaction mining, Bioinformatics 19(1) :125- 134, Jan. 2003
Joint Center for
Structural Genomics Technologies http://www.jcsg.org/scripts/prod/technologies1.html
Nature Structural Biology, Structural genomics supplement, Nov.
2000 http://www.nature.com/nsmb/
glossary index
to look for other unfamiliar terms
IUPAC definitions are
reprinted with the permission of the International Union of Pure and Applied
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01-03-2012, 11:54 PM #10Registered User
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Deadly Connecticut Fire Started by Ashes Removed for Santa
Read more: http://www.foxnews.com/us/2012/01/03...#ixzz1iSTFsRDA
NEW HAVEN, Conn. – "Smoldering embers blamed for a Christmas morning house fire that killed three girls and their grandparents had been taken out of a fireplace so the children would not worry about Santa Claus coming down the chimney, two officials told The Associated Press Tuesday."
"Two officials briefed on the investigation say the ashes were removed out of concerns for Santa. They spoke to The Associated Press on condition of anonymity Tuesday because the investigation is still under way."
"Authorities say embers in a bag of discarded ashes started the blaze in Stamford that killed 10-year-old Lilly and 7-year-old twins Grace and Sarah Badger and their grandparents, Lomer and Pauline Johnson."
"The girls' mother, Madonna Badger, escaped the fire along with a friend, Michael Borcina. Borcina and Badger were treated at a local hospital and released."
"Fire officials have said Borcina is believed to have placed the ashes in or outside an entryway, near the trash."
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GUILTY CO - Timothy, 3, & Alivia Ramirez, 15 mos, home alone, died in fire, 30 Oct 2011By peeples in forum Recently Sentenced and BeyondReplies: 5Last Post: 08-09-2015, 02:12 PM
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subset: commoncrawl


text:
Top Definition
Similar to a "teabag" sexual position, only the stubag involves inserting your entire scrotal sac inside a person's asshole.
Man, Josh fucked that slut 7 ways from Sunday. I heard she actually took the teabag!
viết bởi SA Morris 20 Tháng mười một, 2003
Trending Now
Can you define these popular missing words?
Similar to being a douchebag, but is acceptable to say in public.
That guy sounds like such a douchebag!
No man, he's a Stubag!
No man, he's a Stubag!
viết bởi GWood 11 Tháng mười, 2005
One with the ability to fall down flights of stairs whilst miraculously keeping their entire drink in it's vessel
Oh My God... He did another Stubags!
viết bởi Popsi 10 Tháng hai, 2010
A sexual maneuver in which one man inserts his scrotum into another man's anus. Similar to the dipping motion of a tea bag in cup of hot water.
Last nights stubag left dookie crumbs all over my ass hair.
viết bởi Terrence Ramholt 20 Tháng mười một, 2003


text:
As Listed
Arthur J. Raffles is a character created in the 1890s by E. W. Hornung, a brother-in-law to Arthur Conan Doyle, the creator of Sherlock Holmes. Raffles is, in many ways, a deliberate inversion of Holmes — he is a "gentleman thief," living in The Albany, a very upscale address in London, playing cricket for the Gentlemen of England and supporting himself by carrying out ingenious burglaries. He… (more)


text:
CGI-Perl Tips
How to direct a browser to display a different HTML page This is actually very simple to do in a CGI script. Instead of the usual header
Code: PERL
How to manipulate browser caching
Using an Expires header is the best way of achieving this in most cases. Specify a date in the past, and the browser will think the page must be updated next time it requires it.
You can also specify to certain browsers that they should not cache this document by returning a no-cache pragma.
The pragma is returned as part of your header. For example, your script might return
Code: PERL
Code: PERL
Code: PERL
Some of the more useful environment variables can be fetched through this interface. The methods are as follows:
Return a list of MIME types that the remote browser accepts. If you give this method a single argument corresponding to a MIME type, as in $query->accept('text/html'), it will return a floating point value corresponding to the browser's preference for this type from 0.0 (don't want) to 1.0. Glob types (e.g. text/*) in the browser's accept list are handled correctly.
Returns the HTTP_COOKIE variable, an HTTP extension implemented by Netscape browsers version 1.1 and higher. Cookies have a special format, and this method call just returns the raw form (?cookie dough). See cookie() for ways of setting and retrieving cooked cookies.
Returns the HTTP_USER_AGENT variable. If you give this method a single argument, it will attempt to pattern match on it, allowing you to do something like $query->user_agent(netscape);
Returns additional path information from the script URL. E.G. fetching /cgi-bin/your_script/additional/stuff will result in $query->path_info() returning "additional/stuff".
As per path_info() but returns the additional path information translated into a physical path, e.g. ``/usr/local/etc/httpd/htdocs/additional/stuff''.
Returns either the remote host name or IP address. if the former is unavailable.
Return the script name as a partial URL, for self-refering scripts.
Return the URL of the page the browser was viewing prior to fetching your script. Not available for all browsers.
auth_type ()
Return the authorization/verification method in use for this script, if any.
server_name ()
Returns the name of the server, usually the machine's host name.
virtual_host ()
When using virtual hosts, returns the name of the host that the browser attempted to contact.
server_software ()
Returns the server software and version number.
remote_user ()
Return the authorization/verification name used for user verification, if this script is protected.
user_name ()
Attempt to obtain the remote user's name, using a variety of different techniques. This only works with older browsers such as Mosaic. Netscape does not reliably report the user name!
Returns the method used to access your script, usually one of 'POST', 'GET' or 'HEAD'.
Creating a self-referencing URL which preserves state information:
Code: PERL
Code: PERL
Code: PERL
Code: PERL
|All times are GMT +5.5. The time now is 04:03.


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Hi! My name is Gir
I am a Manx from georgetown, IN
Nicknames: girby, girber, gibby.he is also called rotten boy.
Age: 8 years old
Gender: M
Coat: short haired
Education: climbing up the christmas tree, and knocking over a big cat house!! :)
My favorite tricks and treats are: backflips and i know this is`nt really a trick but, he falls down A LOT! and temptations and cheese.
Where I hang out: in the bathtub. he slides all around in it!
My favorite grubs: leftovers.
My pet peeves: when his food bowl isnt full. he REALLY hates that!
What I love about my owners: she always fills my food bowl up ALL THE WAY!
My cat hobbies: he likes to eat, sleep and play about... hmmm...i`d say only for about 30 minutes.
Pet motto: if anybody gives you food, EAT IT!!
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my cat had a few litters of cats and she hardly ever fed him and so when we got some evaporated milk,he stole some of the other cats milk!
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Travel Gallery
Kangaroo Island
Photo: Mary Ellen Botter/Staff
Each of the 21 suites at Southern Ocean Lodge on Kangaroo Island has a king-sized bed, natural wood accents and floor-to-ceiling windows for watching the waves below the cliff on which the lodge was built.
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Students with Asperger's Syndrome who are
integrated into the inclusive school system
experience different challenges and have needs,
which are dissimilar to their peers. This
qualitative, ethnographic study was designed to
investigate the high school experiences of students
diagnosed with Asperger's Syndrome in one Ontario
school. Data was collected primarily from interviews
with: students with Asperger's Syndrome, non-
identified students, parents of students with
Asperger's Syndrome, regular education teachers,
paraprofessionals, administrators, and members of
the multi-disciplinary team. The data was analyzed
and recommendations were formulated in the following
areas: funding, training specialized programming,
advocacy and support.
Tracey, Brake.
Tracey Brake is an Autism Teacher in the York Region District
School Board. She has been working with students on the Autism
Spectrum for 11 years.


text:
King Estate Wines
King Estate is located southwest of Eugene, Oregon near the town of Lorane. The 820 acre estate provides a spectacular mountain vineyard site with elevations ranging from 800 to 1,100 feet and cool, prevailing northwest winds that moderate vineyard temperatures.
majestic winery, which reflects the architectural tradition of a French
chateau, encompasses approximately 110,000 square feet.
Total production capacity is 400,000
More About King Estate Winery
King Estate has also developed Lorane Grapevines, a state of the art vine propagation facility. Lorane Grapevines, Oregon's largest producer of grafted grapevines, operates as a separate business producing vines grafted on various phylloxera-resistant rootstock. Lorane Grapevines provides rootstock for planting King Estate's vineyards and markets grafted vines to the U.S. wine industry as well. The Estate is owned and fully funded by the King family.
Wine Clubs | Oregon Wine | Washington Wine
Privacy Policy | View Cart | Customer Service | Contact Us | Sign up For Newsletter
503.206.8589 email@example.com
Avalon Wine Inc. 3115 NE Sandy Blvd. #127 Portland, OR 97232


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Learn to Code. Learn to Create.
UCode is the largest after school code learning program in the United States with both online and campus based programs and camps led by teachers. Our project based curriculum teaches kids to create their own apps, websites, games and robots.
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19 Sep 2009
Trying to decide which 2 to start out of the 4:
Colston @ PHI
VJax vs. BAL
Marshall vs. CLE
Burleson @ SF
Mostly ruling Burleson out. Colston and Jackson have tougher matchups, but much more reliable quarterbacks and temperaments. I'm leaning towards those two, but does anyone have a good argument otherwise?
2 replies , Last at 20 Sep 2009, 10:03am by max
There's a good chance Marshall plays up to his talent this week, but I wouldn't like to count on it. Might be best to bench him until after he's proven he'll make an effort.
Clearly, Colston must start. Brees is on fire. I just heard Sean Payton say on WFAN that the ball never touched the ground in their 7 on 7 drills this week.
I'd probably give the nod to VJax over Burleson even though NB looked really fresh last week. Still it was the Rams. And the Niners did a super job on the AZ passing game last week.


text:
It was morning, and already many eyes and hands were on Michelle Holloway.
The 24-year-old model stood in silver heels ever so high, wearing black lingerie that revealed much of her flawless, caramel skin. Her hair tumbled to her shoulders in a swarm of tight curls.
Holloway remained calm, smiling at times, as student designer Aisha Richardson and two faculty members at Moore College of Art and Design pulled, tucked and twisted clothing around her 5-foot-10 frame. She was booked to wear six outfits - including a paisley print cocktail dress and a stunning white, bejeweled swimsuit - in the school's annual fashion show.


text:
Citizens for Safe Technology
Empowering the public to protect children
and nature from unsafe wireless technologies.
News and Developments
WHAT'S NEW: NEWS and DEVELOPMENTS CONTENTS
MAILING ADDRESS for BC HYDRO SMART METER CLASS ACTION:
Coalition to Stop Smart Meters
PO Box 52061
Beacon Ave. RPO
Sidney, BC V8L 5V9
EMAIL address for letters to BCUC: email@example.com
EMAIL address for Greg Reimer, BC HYDRO: firstname.lastname@example.com
Smart Meter Class Action postings, in chronological order, are HERE.
To streamline your search, anywhere on the website, for a specific topic, word or phrase, please use the white search bar located under the Action Kits below.
Looking for a specific topic or a past article? Search for it below:
« Return to News and Developments
Most Political Parties are Against Smart Meters - Why Aren't You?
Roadkill Radio
"Kari Simpson and Ron Gray have already made their stand (and built their cages) to fend off the dangerous, intrusive, and frankly illegal Smart Meters. Now listen to Una St. Clair of Citizens For Safe Technology (.org) about the growing grassroots movement to protect our health, our homes, our privacy, our money, and our civil rights.
"Smart Meters - made in China, assembled in the U.S. - have not been approved for safety by the Canadian Standards Association or Underwriters Laboratory. Your home insurance probably won't cover the damage done to your home when your Smart Meter starts a fire, as many already have. Insurance can never recover the health consequences that Smart Meters have been documented to cause. Your electricity bill may triple - or more! Are you ready to stand up for your rights?
"Are you ready to protect yourself? Are you ready to get smart and Fight Smart Meters?"
One time donation: Click the donate button below and follow the instructions on the screen.
Monthly donation: If you wish to contribute every month, please select the amount from the Donation Options list below and click Subscribe. Your contribution will be sent for you every month for the amount you selected.
Citizens for Safe Technology (CST) is funded and supported solely by those who wish to help us. Thank-you for learning, sharing and helping if you can.
Meetings and events on the issue of wireless technologies in homes and communities throughout North America.
Click the button above to sign our online petition to return to hardwired computers in schools.
Click the button above to sign our online petition against Smart Meters in British Columbia.
Download and print this petition form -- Refuse Smart Meter Installation.
Send completed petitions 15 signatures per page to:
Una St. Clair
e-mail: email@example.com
Download Brochure
Citizens For Safe Technology
"Wi-Fi: Is It Safe?"
About CST
Citizens for Safe Technology is a not-for-profit educational society made up of parents, grandparents, teachers, business professionals, scientists, politicians and lawyers concerned about the exponential increase in public exposure to harmful wireless technologies.
We believe a profound urgency exists to protect the unsuspecting public, especially children, youth and pregnant mothers from unsafe wireless technologies.
The content of the Citizens for Safe Technology website is provided for information purposes only. Information is subject to change without prior notice. Every effort has been taken to ensure that the information on this website is accurate, but no guarantees can be made.
Neither Citizens for Safe Technology nor its authors are liable for damages resulting from the use of information obtained from this site. The authors are not responsible for any contents linked or referred to from this website or any damages resulting from information on those sites.
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We should soon learn the verdict for the Oklahoma soldier charged in connection to the largest leak of classified information in U.S. history.
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Running a business and being a concert promoter are two different jobs. But in both cases, it pays to listen to your customers.
And it was the fans who commented on Facebook that helped shaped the 2012 River Rock at the Amp concert series.
Sunrise Entertainment founders Ken Haidaris and Marty Cohen said they took seriously the feedback they received. That's why Eagles' tribute band 7 Bridges is opening the outdoor concert series and making a return appearance in August.
''Last year the bands that people said 'you gotta bring them back' more than any others were 7 Bridges and Chris Higbee,'' Cohen said. ''So we did.''
Higbee is opening for 7 Bridges on Saturday and he will return as a headliner in July with Boardman country singer Sarah Turner opening for him.
''He's one of the most animated artists we've ever had there,'' Cohen said.
But while the schedule features many familiar names from past years - Zoso (Led Zeppelin), Fins to the Left (Jimmy Buffett), Almost Queen (Queen), Vicious Cycle (Lynyrd Skynyrd) and, returning after a one-year absence, Draw the Line (Aerosmith) - the schedule also hints at what Haidaris sees as the future of the River Rock series.
''I'd like to bring more expensive shows in, do two or three bigger shows a year to change it up,'' Haidaris said.
Cohen added, ''We're upping the ante with MSR (Michael Stanley and the Resonators).''
Stanley sold out Packard Music Hall in 2010 and has a long history as a concert draw in northeast Ohio. His show, which is being co-promoted by Sunrise Entertainment and Packed House Productions, is the first time they've had any reserved seating for a River Rock event. Only about 30 of the 420 reserved VIP and Party Zone tickets remain, Haidaris said, and advance sales have been good for the general admission tickets as well.
''If we get the weather, downtown Warren will be buzzing that night,'' Haidaris said. ''I think that's awesome.''
The promoters attempted to bring one other national act to the venue this summer, and Haidaris said those kinds of shows will create a buzz and bring more people to downtown Warren, which is why the two local businessmen (Cohen is the owner of Mickey's Army-Navy Store, Haidaris is co-owner of the Sunrise Inn) formed Sunrise Entertainment and took over the summer concert series after the death of original promoter Walt English.
''It's such a great facility,'' Haidaris said. ''It's too nice not to bring people to northeast Ohio.''
Haidaris and Cohen aren't worried about increased competition from the Country at the Amp series that will feature tribute acts on Fridays beginning June 8.
Both promoters are sharing costs on things like fencing and portable toilets, which will help lower expenses in some areas, although Haidaris admitted that he's sure there will be some cannibalization because many concertgoers won't want to spend both weekend nights at the amphitheater and will have to pick and choose.
But for two men who've always said their goal was to bring more people downtown, two nights of tribute shows and Fine Arts Council events on Thursdays will create more entertainment options and opportunities for downtown businesses.
Cohen said he believes a thriving arts and entertainment scene is important for the city to grow. It was a topic earlier this week at a Trumbull 100 meeting.
''Those young professional guys who have technical backgrounds, they can go anywhere, live anywhere,'' Cohen said. ''There has to be quality of life (to bring them to Warren). There's more happening here than there was a decade ago, and we need more.''


text:
In Rome, papers will focus on Italian and Southern Europe cities, with contributions from K. Chatzis (Athens), S. Adorno (Syracuse), A. Da Silva (Lisbon), A. Giuntini (Italy), C. Worms (Madrid)...
F. Scherrer, S. Thibault and P. Capuzzo will present papers on the methodological stakes of network analysis under a social point of view.
The results of the whole program will be published by the Ecole francaise de Rome (French Research Center in Rome).
Contact for Technical Networks and Social Networks program: Denis Bocquet. email@example.com


text:
TROY, Mich. -- Kmart here said Ronald J. Floto has resigned as executive vice president and president of Super Kmart Centers, effective May 5. ding Floto on an interim basis will be Floyd Hall, chairman, president and chief executive officer of Kmart. In addition, Ernest L. Heether, senior vice president for merchandising planning and replenishment, will take over Floto's responsibilities for the company's distribution centers. Last week, Dairy Farm International Holdings Ltd. announced it ...
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Monica Vitti, once the rage of Italian cinema, has lately returned to U.S. attention with the so-so An Almost Perfect Affair and now this, a comedy about a small-time thief. She plays a lovable humbler of a con artist who spends as much time in the clink as out. In one hilarious scene she bilks a rich man out of all his lire, only to find that they're counterfeit. The film itself, by cinematographer turned director Carlo Di Palma, does not measure up to Vitti's bravura performance, wandering over the Italian landscape. For an actress best remembered for her distinctive work with director and ex-lover Michelangelo Antonioni (L'Avventura, Red Desert), Vitti seems to be underachieving here. (In Italian with English subtitles) (Not rated)
Picks and Pans Review: Teresa the Thief
updated 06/18/1979 AT 01:00 AM EDT
•originally published 06/18/1979 AT 01:00 AM EDT


text:
OMG. Hilarious. That was nauseating.
OMG. Hilarious. That was nauseating.
Last edited by Robert.O; 12-31-2012 at 02:03 PM.
I somehow disagree with most posters here; the diet advices that she gives on a very general basis are sound and healthy, even if she doesnt look that good herself, which is pretty irrelevant IMO. Its a bit like a coach out of shape himself that gives advices to top sportsmen, and they listen to him because they know that he know the game!
Or maybe you all would have preferred to listen to a dietician that looked like this instead:
(thread nearly 3 years old resurrected by a spammer, by the way )


text:
Hello all!!!
I stumbled upon the Primal Blueprint last week and wish I had a couple years ago. I am an avid exerciser (not chronic by any means, I just love being active everyday) and am steps away from a certification as a Nutritionist. My school is exceptionally progressive in thinking and exposing us to over 100 dietary theories but the thing that got me really excited was the introduction to Paleo and Ancestral eating a few month ago that ultimately led me to The Primal Blueprint. A book which I purchased last Friday and DEVOURED over the weekend.
I recently moved from the heart of the Rocky Mountains to New York City, to be closer to my long-term girlfriend and start a 'real' job. 3 weeks ago, I was hired at Peak Performance NYC as the Director of Sales and Marketing. Peak is a one-on-one personal training studio that REALLY exemplifies the Primal lifestyle (kind of Crossfit but not Crossfit). We haul sand bags, battle ropes, push sleds, and have fun while working out! I couldn't ask for a better job at a better gym!
Why am I telling you all this?? Because, I am embarking on the 30 Day Primal Challenge (I actually began Sunday) and cant wait to test this program. Through Peak, I also now have ALL the tools to do just that. I have been kind of living this lifestyle for years but now have the "Blueprint" that will allow me to make the tweaks I need to hopefully drop the last 10 pounds I have always carried around (Until now I subscribed to the 'whole grains = good grains theory). So, goodbye grains.
I had a full body composition performed on Friday and here are some of the particulars:
Height- 5'9"
Weight- 162.7 pounds
So, as you can see, I'm not in bad shape by any means. I just want to lean out and with the support of the Primal Blueprint, Peak Performance and this community, I think I can do just that! I'll try and update and post often and maybe inspire or guide a fellow 'Grok'.
Welcome. We need primal nutritionists.
Ancestral Health Info
I design websites and blogs for a living. If you would like a blog or website designed by someone who understands Primal, see my web page.
Primal Blueprint Explorer My blog for people who are not into the Grok thing. Since starting the blog, I have moved close to being Archevore instead of Primal. But Mark's Daily Apple is still the best source of information about living an ancestral lifestyle.


text:
In the following video, Motley Fool financials analyst David Hanson takes a look forward at the upcoming CCAR banking stress test results, which will be the basis upon which the Fed decides whether to grant permission to the banks to expand their capital allocation programs through dividend increases and share repurchases. He takes a look at three of the biggest banks receiving results tomorrow, JP Morgan (NYSE: JPM ) , Bank of America (NYSE: BAC ) , and Citigroup (NYSE: C ) , and gives investors the most likely scenario for what, if any, new capital allocations they can expect.
Bank of America's stock doubled in 2012. Is there more yet to come? With significant challenges still ahead, it's critical to have a solid understanding of this megabank before adding it to your portfolio. In The Motley Fool's premium research report on B of A, analysts Anand Chokkavelu, CFA, and Financials Bureau Chief Matt Koppenheffer lift the veil on the bank's operations, including detailing three reasons to buy and three reasons to sell. Click here now to claim your copy.