the wwpdb ( 1 ) maintains the protein data bank ( pdb ) archives of biological macromolecular structure data , currently comprising over 32500 structures . since the year 2000 , the worldwide structural genomics initiatives have provided more than 2400 structures , which have also added a large number of new folds . to represent the progress of this collective effort , the rcsb pdb ( 2 ) has developed and maintains the structural genomics information portal at   which consists of three main sections , outlined below . the first section of the information portal provides summary information about each structural genomics center , including target lists , target status , targets in the pdb and sequence redundancy analyses . summary statistics describing the overall progress of all contributing projects , including sequence similarity and number of structures determined , are regularly tabulated . as an example , an analysis of the sequence similarity of structures solved by structural genomics projects relative to structures in the pdb archive is shown in figure 1 . the targets section offers databases that track target registration data . currently , 20 structural genomics centers contribute data to the targetdb ( 3 ) resource ( ) . these data include contributing project and target identifier ; protein name , source organism and sequence ; current production status ( e.g. cloned , expressed and crystallized ) ; related database references ; and links to related project information . targetdb assembles data from all contributing centers and makes these data available in a single validated xml data file which is updated weekly . targets can also be selected by searching targetdb by target identifier , similar sequence , program or project , current production status , protein name or source organism . the html report presents all of the contributed details about each target including links to related project information and archival databases [ e.g. sequence , pdb and bmrb ( 4 ) ] , and links out to protein domain databases . an additional online form constructs cumulative reports summarizing the status of a particular program or project . created as an extension to targetdb , the protein expression cloning and purification database , pepcdb ( ) , was established to collect more detailed status information and the experimental details of each step in the protein production pipeline . pepcdb captures a complete history of the experimental steps in each production trial , in addition to describing the current target production status . the status history in pepcdb also records the time interval required to complete each experimental step , with an explanation if work on a particular target or experiment was terminated . each trial may reference a set of standard protocols and optionally include the special details of an experimental step and the experimentally observed sequence . pepcdb currently includes protocol information from the nih protein structure initiative ( psi ) centers . targetdb status data from all other structural genomics centers are merged into pepcdb . as a result , pepcdb always provides the most complete view of target status and experimental information for structural genomics projects . the search features of pepcdb build upon those of targetdb by offering additional tools to mine experimental protocols . the resulting report includes the essential target description provided by targetdb plus additional links to a chronological status history and links to related experimental protocols . the structures section of the rcsb pdb structural genomics information portal ( ) provides information about the functional distribution of solved structures , structures being determined by structural genomics and homology models determined from solved structures ( 5 ) . function is measured relative to ensembl - assigned functions from the human genome ( 6 ) and disease relative to omim assignments for human diseases ( 7 ) . this section answers the question  with respect to the function of proteins identified in humans and human disease , what does the present complement of structures in the pdb , the structural genomics targets ( if all were solved ) and homology models that can be built from the current set of templates add to our understanding of living systems? the answer to this question changes over time , and the functional distribution resource provides a current answer since the constituent components needed to address the question  pdb structures , structural genomics targets , homology models from superfamily ( 8) , functional assignments from ensembl and disease classifications from omim  are all updated as they change , ranging from weekly for pdb structures and targets to approximately annually for superfamily . the answer to the question also depends on the definition of a homology model . here the structural templates used in homology modeling were a set of hidden markov models taken from superfamily 1.65 . the sequences were aligned to the structural template with hmmer ( 9 ) . only those assigned domains with sequence identity > 30% in the alignment were considered as homology models . through the functional distribution site , this question can be addressed by examining molecular function , biological process and cellular component [ as assigned by the gene ontology , go ( 10 ) ] , enzymes via their ec numbers ( ) , and diseases assigned through omim ( 7 ) . several steps are used to define the search parameters ; here molecular function is used as an example . in step 1 ( molecular function ) the breadth of the search is defined , which in turn defines the details presented in the results . so , for example , the top level of the go hierarchy for molecular function is displayed and used by default . all structures could be selected , or a subgroup could be selected ( e.g. all structures with the molecular function similarly in step 2 ( structure type ) , all structures are chosen by default , but it is possible to drill down and explore just groups of structures based on the scop classification of class ( all alpha , all beta , etc . ) ( 11 ) . sequence identity defines how the human genome sequences are clustered and a single function assigned for that cluster  at lower sequence identity there are fewer clusters , i.e. the results are effectively at lower resolution . step 5 specifies the domain combinations needed for a match . since pdb structures frequently represent a single domain in a larger complex , statistics can be produced requiring overlap for one or more domains up to the whole structure accounting for domain rearrangements [ see ( 5 ) for a full description ] . based on these input parameters , one of three distributions can be generated : a comparison of the distribution of pdb structures , structure genomics targets or homology models against the human genome ; a  most wanted list of structures those not in the pdb and which ( by default ) are not identified through homology modeling or in the structural genomics targets yet have significant presence in the human genome ; and simple charts showing the distribution of the genome sequences , pdb structures , structural genomics targets or homology models . most distributions are accompanied by two tables illustrating , first , the functional coverage by each data type ( table 1 ) , and second , the correlation between input data types ( data not shown ) . the actual overlap between these groups will be added as part of an on - going development . for example in table 1 , pdb structures cover 37.2% of the identified molecular functions in the human genome ; if solved , structural genomics targets cover 32.4% of functions ; and 56.3% of the molecular functions can be modeled from existing structures . figure 2 illustrates the resulting normalized distributions for the top level of the go molecular function hierarchy . at this level most distributions are not skewed with the exception of molecular function unknown  pdb structures are underrepresented and structural genomics targets are overrepresented . not surprising , since until structural genomics began structural biology was dominated by determining structures of known function . in the era of structural genomics , drilling down to more detailed descriptions of molecular function ( data not shown ) reveals a more uneven distribution and suggests changes in structure determination strategies . an important feature of this resource is the  most wanted list of structures based on the following criteria : ( i ) functional categories where proteins are underrepresented by structures ; ( ii ) from ( i ) , proteins which can not be modeled , i.e. proteins from the human genome without superfamily assignments ; ( iii ) if the protein can be associated with a human disease ; and ( iv ) proteins identified as likely to be intractable , i.e. with a transmembrane segment filtered out . the first section of the information portal provides summary information about each structural genomics center , including target lists , target status , targets in the pdb and sequence redundancy analyses . summary statistics describing the overall progress of all contributing projects , including sequence similarity and number of structures determined , are regularly tabulated . as an example , an analysis of the sequence similarity of structures solved by structural genomics projects relative to structures in the pdb archive is shown in figure 1 . the targets section offers databases that track target registration data . currently , 20 structural genomics centers contribute data to the targetdb ( 3 ) resource ( ) . these data include contributing project and target identifier ; protein name , source organism and sequence ; current production status ( e.g. cloned , expressed and crystallized ) ; related database references ; and links to related project information . targetdb assembles data from all contributing centers and makes these data available in a single validated xml data file which is updated weekly . targets can also be selected by searching targetdb by target identifier , similar sequence , program or project , current production status , protein name or source organism . the html report presents all of the contributed details about each target including links to related project information and archival databases [ e.g. sequence , pdb and bmrb ( 4 ) ] , and links out to protein domain databases . an additional online form constructs cumulative reports summarizing the status of a particular program or project . created as an extension to targetdb , the protein expression cloning and purification database , pepcdb ( ) , was established to collect more detailed status information and the experimental details of each step in the protein production pipeline . pepcdb captures a complete history of the experimental steps in each production trial , in addition to describing the current target production status . the status history in pepcdb also records the time interval required to complete each experimental step , with an explanation if work on a particular target or experiment was terminated . each trial may reference a set of standard protocols and optionally include the special details of an experimental step and the experimentally observed sequence . pepcdb currently includes protocol information from the nih protein structure initiative ( psi ) centers . targetdb status data from all other structural genomics centers are merged into pepcdb . as a result , pepcdb always provides the most complete view of target status and experimental information for structural genomics projects . the search features of pepcdb build upon those of targetdb by offering additional tools to mine experimental protocols . the resulting report includes the essential target description provided by targetdb plus additional links to a chronological status history and links to related experimental protocols . the structures section of the rcsb pdb structural genomics information portal ( ) provides information about the functional distribution of solved structures , structures being determined by structural genomics and homology models determined from solved structures ( 5 ) . function is measured relative to ensembl - assigned functions from the human genome ( 6 ) and disease relative to omim assignments for human diseases ( 7 ) . this section answers the question  with respect to the function of proteins identified in humans and human disease , what does the present complement of structures in the pdb , the structural genomics targets ( if all were solved ) and homology models that can be built from the current set of templates add to our understanding of living systems? the answer to this question changes over time , and the functional distribution resource provides a current answer since the constituent components needed to address the question  pdb structures , structural genomics targets , homology models from superfamily ( 8) , functional assignments from ensembl and disease classifications from omim  are all updated as they change , ranging from weekly for pdb structures and targets to approximately annually for superfamily . the answer to the question also depends on the definition of a homology model . here the structural templates used in homology modeling were a set of hidden markov models taken from superfamily 1.65 . the sequences were aligned to the structural template with hmmer ( 9 ) . only those assigned domains with sequence identity > 30% in the alignment were considered as homology models . through the functional distribution site , this question can be addressed by examining molecular function , biological process and cellular component [ as assigned by the gene ontology , go ( 10 ) ] , enzymes via their ec numbers ( ) , and diseases assigned through omim ( 7 ) . several steps are used to define the search parameters ; here molecular function is used as an example . in step 1 ( molecular function ) the breadth of the search is defined , which in turn defines the details presented in the results . so , for example , the top level of the go hierarchy for molecular function is displayed and used by default . all structures could be selected , or a subgroup could be selected ( e.g. all structures with the molecular function similarly in step 2 ( structure type ) , all structures are chosen by default , but it is possible to drill down and explore just groups of structures based on the scop classification of class ( all alpha , all beta , etc . ) ( 11 ) . sequence identity defines how the human genome sequences are clustered and a single function assigned for that cluster  at lower sequence identity there are fewer clusters , i.e. the results are effectively at lower resolution . since pdb structures frequently represent a single domain in a larger complex , statistics can be produced requiring overlap for one or more domains up to the whole structure accounting for domain rearrangements [ see ( 5 ) for a full description ] . based on these input parameters , one of three distributions can be generated : a comparison of the distribution of pdb structures , structure genomics targets or homology models against the human genome ; a  most wanted list of structures  those not in the pdb and which ( by default ) are not identified through homology modeling or in the structural genomics targets yet have significant presence in the human genome ; and simple charts showing the distribution of the genome sequences , pdb structures , structural genomics targets or homology models . most distributions are accompanied by two tables illustrating , first , the functional coverage by each data type ( table 1 ) , and second , the correlation between input data types ( data not shown ) . the actual overlap between these groups will be added as part of an on - going development . for example in table 1 , pdb structures cover 37.2% of the identified molecular functions in the human genome ; if solved , structural genomics targets cover 32.4% of functions ; and 56.3% of the molecular functions can be modeled from existing structures . figure 2 illustrates the resulting normalized distributions for the top level of the go molecular function hierarchy . at this level most distributions are not skewed with the exception of molecular function unknown  pdb structures are underrepresented and structural genomics targets are overrepresented . not surprising , since until structural genomics began structural biology was dominated by determining structures of known function . in the era of structural genomics , drilling down to more detailed descriptions of molecular function ( data not shown ) reveals a more uneven distribution and suggests changes in structure determination strategies . an important feature of this resource is the  most wanted list of structures based on the following criteria : ( i ) functional categories where proteins are underrepresented by structures ; ( ii ) from ( i ) , proteins which can not be modeled , i.e. proteins from the human genome without superfamily assignments ; ( iii ) if the protein can be associated with a human disease ; and ( iv ) proteins identified as likely to be intractable , i.e. with a transmembrane segment filtered out . in this report , we present the resources currently made available through the rcsb pdb in support of the structural genomics effort . it is expected that further functionality will be added as the second phase of the psi and other worldwide efforts move forward . august 2005 report from the structural genomics information portal showing structural genomics structures with sequence similarity < 30% relative to solved structures in the pdb by year . normalized functional coverage of the human genome by sequence ( from ensembl ; red ) , by structures from the pdb ( blue ) , by structural genomics targets ( green ) and homology models from superfamily ( yellow ) . when viewing the figure from the online structural genomics portal , clicking on the appropriate bar of the histogram will produce a list of sequences or structures that define the distribution . data are based upon 10801 functionally described human genome sequences from ensembl , 942 pdb structures from human , 1680 structural genomics targets identified in human and 2823 homology models from superfamily mapped on to the human genome . cluster coverage is the ratio of number of protein clusters that are structurally covered versus all clusters in the genome for a functional class with a specified sequence identity ( 40% in this case ) .
the rcsb protein data bank ( pdb ) offers online tools , summary reports and target information related to the worldwide structural genomics initiatives from its portal at . 
 there are currently three components to this site : structural genomics initiatives contains information and links on each structural genomics site , including progress reports , target lists , target status , targets in the pdb and level of sequence redundancy ; targets provides combined target information , protocols and other data associated with protein structure determination ; and structures offers an assessment of the progress of structural genomics based on the functional coverage of the human genome by pdb structures , structural genomics targets and homology models . 
 functional coverage can be examined according to enzyme classification , gene ontology ( biological process , cell component and molecular function ) and disease .