Shape complementarity at protein interfaces via global docking optimisation

被引：2

作者：

Williams, Gareth ^{[1
]}

机构：

[1] Kings Coll London, Bioinformat, Wolfson CARD, Hodgkin Bldg, London SE1 1UL, England

来源：

JOURNAL OF MOLECULAR GRAPHICS & MODELLING | 2018年 / 84卷

关键词：

Protein structure; Protein-protein docking; Shape complementarity; RECOGNITION; POTENTIALS; MODELS; FOLD;

D O I：

10.1016/j.jmgm.2018.06.011

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Protein complexes are characterised by shape complementarity at the interface. Here we present a simple fast global shape fitting algorithm to investigate the extent to which interfaces are global minima of complementarity. The algorithm is applied to a varied set of hetero and homo complexes and complexes between complexes showing that over 90% of large interfaces are global maxima in the space of shape complementarity. Crown Copyright (C) 2018 Published by Elsevier Inc. All rights reserved.

引用

页码：69 / 73

页数：5

共 27 条

[1] Principles of flexible protein-protein docking [J].

Andrusier, Nelly ;

Mashiach, Efrat ;

Nussinov, Ruth ;

Wolfson, Haim J. .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2008, 73 (02) :271-289

[2] Dissecting subunit interfaces in homodimeric proteins [J].

Bahadur, RP ;

Chakrabarti, P ;

Rodier, F ;

Janin, J .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 53 (03) :708-719

[3] CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics [J].

Basu, Sankar .

JOURNAL OF MOLECULAR MODELING, 2018, 24 (01)

[4] Finding correct protein-protein docking models using ProQDock [J].

Basu, Sankar ;

Wallner, Bjorn .

BIOINFORMATICS, 2016, 32 (12) :262-270

[5] ClusPro: a fully automated algorithm for protein-protein docking [J].

Comeau, SR ;

Gatchell, DW ;

Vajda, S ;

Camacho, CJ .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W96-W99

[6] MolProbity: all-atom contacts and structure validation for proteins and nucleic acids [J].

Davis, Ian W. ;

Leaver-Fay, Andrew ;

Chen, Vincent B. ;

Block, Jeremy N. ;

Kapral, Gary J. ;

Wang, Xueyi ;

Murray, Laura W. ;

Arendall, W. Bryan, III ;

Snoeyink, Jack ;

Richardson, Jane S. ;

Richardson, David C. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W375-W383

[7] Modelling protein docking using shape complementarity, electrostatics and biochemical information [J].

Gabb, HA ;

Jackson, RM ;

Sternberg, MJE .

JOURNAL OF MOLECULAR BIOLOGY, 1997, 272 (01) :106-120

[8] An iterative knowledge-based scoring function for protein-protein recognition [J].

Huang, Sheng-You ;

Zou, Xiaoqin .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2008, 72 (02) :557-579

[9] Structure-derived potentials and protein simulations [J].

Jernigan, RL ;

Bahar, I .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 1996, 6 (02) :195-209

[10] PROTEIN-PROTEIN INTERACTIONS - A REVIEW OF PROTEIN DIMER STRUCTURES [J].

JONES, S ;

THORNTON, JM .

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 1995, 63 (01) :31-+

← 1 2 3 →