Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in real time is a crucial research issue. In this paper, we present a novel and effective scoring scheme that is dependent on novel features extracted from protein alpha carbon distance matrices. Our scoring scheme is inspired from pattern recognition and computer vision. Our method is significantly better than the current state of the art methods in terms of family match of pairs of protein structures and other statistical measurements. The effectiveness of our method is tested on standard benchmark structures. A web service is available at this http URL where you can get the similarity measurement score between two protein structures based on our method.
@cite_19: Here we present a novel technique for the alignment of flexible proteins. The method does not require an a priori knowledge of the flexible hinge regions. The FlexProt algorithm simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. Our technique is not sensitive to insertions and deletions. Numerous methods have been developed to solve rigid structural comparisons. Unlike FlexProt, all previously developed methods designed to solve the protein flexible alignment require an a priori knowledge of the hinge regions. The FlexProt method is based on 3-D pattern-matching algorithms combined with graph theoretic techniques. The algorithm is highly efficient. For example, it performs a structural comparison of a pair of proteins with 300 amino acids in about 7 s on a 400-MHz desktop PC. We provide experimental results obtained with this algorithm. First, we flexibly align pairs of proteins taken from the database of motions. These are extended by taking additional proteins from the same SCOP family. Next, we present some of the results obtained from exhaustive all-against-all flexible structural comparisons of 1329 SCOP family representatives. Our results include relatively high-scoring flexible structural alignments between the C-terminal merozoite surface protein vs. tissue factor; class II aminoacyl-tRNA synthase, histocompatibility antigen vs. neonatal FC receptor; tyrosine-protein kinase C-SRC vs. haematopoetic cell kinase (HCK); tyrosine-protein kinase C-SRC vs. titine protein (autoinhibited serine kinase domain); and tissue factor vs. hormone-binding protein. These are illustrated and discussed, showing the capabilities of this structural alignment algorithm, which allows un-predefined hinge-based motions. Proteins 2002;48:242–256. © 2002 Wiley-Liss, Inc.
@cite_27: Motivation: Protein structures are flexible and undergo structural rearrangements as part of their function, and ye tm ost existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment. Results: We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment of proteins. The FATCAT approach simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference protein. In contrast, currently existing flexible structure alignment programs treat the hinge detection as a post-process of a standard rigid body alignment. We illustrate the advantages of the FATCAT approach by several examples of comparison between proteins known to adopt different conformations, where the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges.
FATCAT @cite_27 or lexible structure lignmen by haining ligned fragment pairs with wists is a unique approach in a sense that it took the structural rearrangements that the proteins go through into account. This is different as in most methods the structure is treated like a fixed body. In comparison with other concurrent methods like FlexProt @cite_19 and other rigid body approaches it produced good results in most cases.