TOP: a new method for protein structure comparisons and similarity searches

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 Cα 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.

[1]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[2]  G. Kleywegt,et al.  Detecting folding motifs and similarities in protein structures. , 1997, Methods in enzymology.

[3]  G. Schneider,et al.  Crystal structure of β‐ketoacyl‐acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes , 1998, The EMBO journal.

[4]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[5]  P Willett,et al.  Use of techniques derived from graph theory to compare secondary structure motifs in proteins. , 1990, Journal of molecular biology.

[6]  Gunter Schneider,et al.  High Resolution Crystal Structure of Pyruvate Decarboxylase from Zymomonas mobilis , 1998, The Journal of Biological Chemistry.

[7]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[8]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[9]  P Argos,et al.  Exploring structural homology of proteins. , 1976, Journal of molecular biology.

[10]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[11]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[12]  T. Blundell,et al.  Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. , 1990, Journal of molecular biology.

[13]  M G Rossmann,et al.  Comparison of protein structures. , 1985, Methods in enzymology.

[14]  Robert Huber,et al.  Die automatisierte Faltmolekülmethode , 1965 .

[15]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[16]  Cristofer Enroth.  The structure of phenol hydroxylase and its relation to other flavoenzymes , 1998 .

[17]  P Willett,et al.  Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. , 1993, Journal of molecular biology.

[18]  D Fischer,et al.  Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures , 1996, Proteins.