Searching for patterns of amino acids in 3D protein structures

被引：61

作者：

Spriggs, RV

Artymiuk, PJ

Willett, P ^{[1
]}

机构：

[1] Univ Sheffield, Krebs Inst Biomol Res, Sheffield S10 2TN, S Yorkshire, England

[2] Univ Sheffield, Dept Informat Studies, Sheffield S10 2TN, S Yorkshire, England

[3] Univ Sheffield, Dept Mol Biol & Biotechnol, Sheffield S10 2TN, S Yorkshire, England

来源：

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES | 2003年 / 43卷 / 02期

关键词：

D O I：

10.1021/ci0255984

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

This paper describes the program ASSAM, which has been developed to search for patterns of amino acid side-chains in the 3D structures in the Protein Data Bank. ASSAM represents an amino acid by a vector drawn from the main chain towards the functional part of the amino acid and then computes a graph representation of a protein in which the individual side-chain vectors are the nodes and the intervector distances are the edges. The presence of a query pattern in a Protein Data Bank structure can then be searched for by means of a subgraph isomorphism algorithm. Recent enhancements to ASSAM allow searches to include the following: the main-chain structure in addition to the side-chains; the secondary structure and solvent accessibility of side-chains; allowable distances from a known binding-site; disulfide bridges; and improved generic and wild-card queries. The effectiveness of these approaches is demonstrated by extensive searches of the Protein Data Bank for typical 3D query patterns.

引用

页码：412 / 421

页数：10

共 31 条

[1] IDENTIFICATION OF BETA-SHEET MOTIFS, OF PSI-LOOPS, AND OF PATTERNS OF AMINO-ACID-RESIDUES IN 3-DIMENSIONAL PROTEIN STRUCTURES USING A SUBGRAPH-ISOMORPHISM ALGORITHM [J].

ARTYMIUK, PJ ;

GRINDLEY, HM ;

POIRRETTE, AR ;

RICE, DW ;

UJAH, EC ;

WILLETT, P .

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1994, 34 (01) :54-62

[2] A GRAPH-THEORETIC APPROACH TO THE IDENTIFICATION OF 3-DIMENSIONAL PATTERNS OF AMINO-ACID SIDE-CHAINS IN PROTEIN STRUCTURES [J].

ARTYMIUK, PJ ;

POIRRETTE, AR ;

GRINDLEY, HM ;

RICE, DW ;

WILLETT, P .

JOURNAL OF MOLECULAR BIOLOGY, 1994, 243 (02) :327-344

[3] THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].

BAILEY, S .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763

[4] The Protein Data Bank [J].

Berman, HM ;

Battistuz, T ;

Bhat, TN ;

Bluhm, WF ;

Bourne, PE ;

Burkhardt, K ;

Iype, L ;

Jain, S ;

Fagan, P ;

Marvin, J ;

Padilla, D ;

Ravichandran, V ;

Schneider, B ;

Thanki, N ;

Weissig, H ;

Westbrook, JD ;

Zardecki, C .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :899-907

[5] High-throughput crystallography for lead discovery in drug design [J].

Blundell, TL ;

Jhoti, H ;

Abell, C .

NATURE REVIEWS DRUG DISCOVERY, 2002, 1 (01) :45-54

[6] STRUCTURE AND MOLECULAR-MODEL REFINEMENT OF RHIZOMUCOR-MIEHEI TRIACYLGLYCERIDE LIPASE - A CASE-STUDY OF THE USE OF SIMULATED ANNEALING IN PARTIAL MODEL REFINEMENT [J].

BRZOZOWSKI, AM ;

DEREWENDA, ZS ;

DODSON, EJ ;

DODSON, GG ;

TURKENBURG, JP .

ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 1992, 48 :307-319

[7]

Christendat D, 2000, NAT STRUCT BIOL, V7, P903

[8] CRYSTAL-STRUCTURE OF VIBRIO-CHOLERAE NEURAMINIDASE REVEALS DUAL LECTIN-LIKE DOMAINS IN ADDITION TO THE CATALYTIC DOMAIN [J].

CRENNELL, S ;

GARMAN, E ;

LAVER, G ;

VIMR, E ;

TAYLOR, G .

STRUCTURE, 1994, 2 (06) :535-544

[9] THE MIDAS DISPLAY SYSTEM [J].

FERRIN, TE ;

HUANG, CC ;

JARVIS, LE ;

LANGRIDGE, R .

JOURNAL OF MOLECULAR GRAPHICS, 1988, 6 (01) :13-&

[10] IDENTIFICATION OF TERTIARY STRUCTURE RESEMBLANCE IN PROTEINS USING A MAXIMAL COMMON SUBGRAPH ISOMORPHISM ALGORITHM [J].

GRINDLEY, HM ;

ARTYMIUK, PJ ;

RICE, DW ;

WILLETT, P .

JOURNAL OF MOLECULAR BIOLOGY, 1993, 229 (03) :707-721

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