Voronoi and Voronoi-related tessellations in studies of protein structure and interaction

被引：140

作者：

Poupon, A ^{[1
]}

机构：

[1] CNRS, Lab Enzymol & Biochim Struct, F-91198 Gif Sur Yvette, France

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2004年 / 14卷 / 02期

关键词：

D O I：

10.1016/j.sbi.2004.03.010

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The three-dimensional structure of a protein can be modeled by a set of polyhedra drawn around its atoms or residues. The tessellation invented by Voronoi in 1908, and other tessellations of space derived from it, provide versatile representations of three-dimensional structures. In recent years, they have been used to investigate a series of issues relating to proteins: atom and residue volumes, packing, folding, interactions and binding.

引用

页码：233 / 241

页数：9

共 60 条

[1] Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins [J].

Adamian, L ;

Liang, J .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 311 (04) :891-907

[2] Higher-order interhelical spatial interactions in membrane proteins [J].

Adamian, L ;

Jackups, R ;

Binkowski, TA ;

Liang, J .

JOURNAL OF MOLECULAR BIOLOGY, 2003, 327 (01) :251-272

[3] Nonatomic solvent-driven Voronoi tessellation of proteins: An open tool to analyze protein folds [J].

Angelov, B ;

Sadoc, JF ;

Jullien, R ;

Soyer, A ;

Mornon, JP ;

Chomilier, J .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2002, 49 (04) :446-456

[4]

BANDYOPHADHYAY D, 2004, IN PRESS S DISCR ALG

[5] A new topological method to measure protein structure similarity [J].

Bostick, D ;

Vaisman, II .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2003, 304 (02) :320-325

[6] VORONOI BINDING-SITE MODEL OF A POLYCYCLIC AROMATIC HYDROCARBON BINDING-PROTEIN [J].

BOULU, LG ;

CRIPPEN, GM ;

BARTON, HA ;

KWON, HJ ;

MARLETTA, MA .

JOURNAL OF MEDICINAL CHEMISTRY, 1990, 33 (02) :771-775

[7] VORONOI MODELING - THE BINDING OF TRIAZINES AND PYRIMIDINES TO LACTOBACILLUS-CASEI DIHYDROFOLATE-REDUCTASE [J].

BRADLEY, MP ;

CRIPPEN, GM .

JOURNAL OF MEDICINAL CHEMISTRY, 1993, 36 (21) :3171-3177

[8] Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations [J].

Carter, CW ;

LeFebvre, BC ;

Cammer, SA ;

Tropsha, A ;

Edgell, MH .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 311 (04) :625-638

[9] A procedure for detection and quantitation of cavity volumes in proteins - Application to measure the strength of the hydrophobic driving force in protein folding [J].

Chakravarty, S ;

Bhinge, A ;

Varadarajan, R .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2002, 277 (35) :31345-31353

[10]

Crippen G M, 1991, NIDA Res Monogr, V112, P7

← 1 2 3 4 5 6 →