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TOP : a new method for protein structure comparisons and similarity searches
Author(s) -
Lu Guoguang
Publication year - 2000
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889899012339
Subject(s) - software , computer science , interface (matter) , structural bioinformatics , ranking (information retrieval) , protein data bank , web server , similarity (geometry) , protein structure database , protein structure , structural alignment , protein structure prediction , the internet , database , data mining , user interface , sequence alignment , protein methods , data structure , sequence database , information retrieval , sequence analysis , peptide sequence , biology , artificial intelligence , world wide web , programming language , image (mathematics) , parallel computing , biochemistry , bubble , maximum bubble pressure method , gene
In order to facilitate the three‐dimensional structure comparison of proteins, software for making comparisons and searching for similarities to protein structures in databases has been developed. The program identifies the residues that share similar positions of both main‐chain and side‐chain atoms between two proteins. The unique functions of the software also include database processing via Internet‐ and Web‐based servers for different types of users. The developed method and its friendly user interface copes with many of the problems that frequently occur in protein structure comparisons, such as detecting structurally equivalent residues, misalignment caused by coincident match of C α atoms, circular sequence permutations, tedious repetition of access, maintenance of the most recent database, and inconvenience of user interface. The program is also designed to cooperate with other tools in structural bioinformatics, such as the 3DB Browser software [Prilusky (1998). Protein Data Bank Q. Newslett. 84 , 3–4] and the SCOP database [Murzin, Brenner, Hubbard & Chothia (1995). J. Mol. Biol. 247 , 536–540], for convenient molecular modelling and protein structure analysis. A similarity ranking score of `structure diversity' is proposed in order to estimate the evolutionary distance between proteins based on the comparisons of their three‐dimensional structures. The function of the program has been utilized as a part of an automated program for multiple protein structure alignment. In this paper, the algorithm of the program and results of systematic tests are presented and discussed.