Principles of flexible protein-protein docking

被引:172
作者
Andrusier, Nelly [1 ]
Mashiach, Efrat [1 ]
Nussinov, Ruth [2 ,3 ]
Wolfson, Haim J. [1 ]
机构
[1] Tel Aviv Univ, Sch Comp Sci, Raymond & Beverly Sackler Fac Exact Sci, IL-69978 Tel Aviv, Israel
[2] SAIC Frederick Inc, Basic Res Program, Ctr Canc Res Nanobiol Program NCI Frederick, Frederick, MD 21702 USA
[3] Tel Aviv Univ, Sackler Fac Med, Dept Human Genet & Mol Med, IL-69978 Tel Aviv, Israel
基金
以色列科学基金会; 美国国家卫生研究院;
关键词
flexible docking; backbone flexibility; side-chain refinement; rigid-body optimization; modeling protein-protein docking;
D O I
10.1002/prot.22170
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
Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem.
引用
收藏
页码:271 / 289
页数:19
相关论文
共 160 条
[61]   Gaussian dynamics of folded proteins [J].
Haliloglu, T ;
Bahar, I ;
Erman, B .
PHYSICAL REVIEW LETTERS, 1997, 79 (16) :3090-3093
[62]   Principles of docking: An overview of search algorithms and a guide to scoring functions [J].
Halperin, I ;
Ma, BY ;
Wolfson, H ;
Nussinov, R .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 47 (04) :409-443
[63]  
Hayward S, 1998, PROTEINS, V30, P144, DOI 10.1002/(SICI)1097-0134(19980201)30:2<144::AID-PROT4>3.0.CO
[64]  
2-N
[65]   METHODS OF CONJUGATE GRADIENTS FOR SOLVING LINEAR SYSTEMS [J].
HESTENES, MR ;
STIEFEL, E .
JOURNAL OF RESEARCH OF THE NATIONAL BUREAU OF STANDARDS, 1952, 49 (06) :409-436
[66]  
Hinsen K, 1998, PROTEINS, V33, P417, DOI 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO
[67]  
2-8
[68]  
HOLM L, 1992, STRUCT FUNCT GENET, V14, P213
[69]   SIDE-CHAIN PREDICTION BY NEURAL NETWORKS AND SIMULATED ANNEALING OPTIMIZATION [J].
HWANG, JK ;
LIAO, WF .
PROTEIN ENGINEERING, 1995, 8 (04) :363-370
[70]   Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem [J].
Jackson, RM ;
Gabb, HA ;
Sternberg, MJE .
JOURNAL OF MOLECULAR BIOLOGY, 1998, 276 (01) :265-285