Protein-Protein Interaction Analysis by Docking

被引:2
作者
Fink, Florian [1 ]
Ederer, Stephan [1 ]
Gronwald, Wolfram [1 ]
机构
[1] Univ Regensburg, Inst Funct Gen, Josef Engert Str 9, D-93053 Regensburg, Germany
关键词
Protein-protein docking; verification of protein interactions; 3D protein structures;
D O I
10.3390/a2010429
中图分类号
TP18 [人工智能理论];
学科分类号
081104 ; 0812 ; 0835 ; 1405 ;
摘要
Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach.
引用
收藏
页码:429 / 436
页数:8
相关论文
共 10 条
[1]   Ten thousand interactions for the molecular biologist [J].
Aloy, P ;
Russell, RB .
NATURE BIOTECHNOLOGY, 2004, 22 (10) :1317-1321
[2]   Interrogating protein interaction networks through structural biology [J].
Aloy, P ;
Russell, RB .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (09) :5896-5901
[3]   Structure-based evaluation of in silico predictions of protein-protein interactions using comparative docking [J].
Cockell, Simon J. ;
Oliva, Baldo ;
Jackson, Richard M. .
BIOINFORMATICS, 2007, 23 (05) :573-581
[4]   HADDOCK: A protein-protein docking approach based on biochemical or biophysical information [J].
Dominguez, C ;
Boelens, R ;
Bonvin, AMJJ .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2003, 125 (07) :1731-1737
[5]   Protein-protein docking benchmark 2.0: An update [J].
Mintseris, J ;
Wiehe, K ;
Pierce, B ;
Anderson, R ;
Chen, R ;
Janin, J ;
Weng, ZP .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 60 (02) :214-216
[6]   Recent progress and future directions in protein-protein docking [J].
Ritchie, David W. .
CURRENT PROTEIN & PEPTIDE SCIENCE, 2008, 9 (01) :1-15
[7]   Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions [J].
Schumann, Frank H. ;
Riepl, Hubert ;
Maurer, Till ;
Gronwald, Wolfram ;
Neidig, Klaus-Peter ;
Kalbitzer, Hans Robert .
JOURNAL OF BIOMOLECULAR NMR, 2007, 39 (04) :275-289
[8]   Classification of protein complexes based on docking difficulty [J].
Vajda, S .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 60 (02) :176-180
[9]   Comparative assessment of large-scale data sets of protein-protein interactions [J].
von Mering, C ;
Krause, R ;
Snel, B ;
Cornell, M ;
Oliver, SG ;
Fields, S ;
Bork, P .
NATURE, 2002, 417 (6887) :399-403
[10]   The Protein Data Bank and structural genomics [J].
Westbrook, J ;
Feng, ZK ;
Chen, L ;
Yang, HW ;
Berman, HM .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :489-491