A protein-protein docking algorithm dependent on the type of complexes.
An efficient 'soft docking' algorithm is described to assist the prediction of protein-protein association using three-dimensional structures of molecules. The basic tools are the 'simplified protein' model and the docking algorithm of Wodak and Janin. The side chain flexibility of Arg, Lys, Asp, Glu and Met residues at the protein surface is taken into account. The complex type-dependent filtering technique on the basis of the geometric matching, hydrophobicity and electrostatic complementarity is used to select candidate binding modes. Subsequently, we calculate a scoring function which includes electrostatic and desolvation energy terms. In the 44 complexes tested including enzyme-inhibitor, antibody-antigen and other complexes, native-like structures were all found, of which 30 were ranked in the top 20. Thus, our soft docking algorithm has the potential to predict protein-protein recognition.
Li
Chun Hua
CH
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China.
Ma
Xiao Hui
XH
Chen
Wei Zu
WZ
Wang
Cun Xin
CX
D000465:Algorithms; D000936:Antigen-Antibody Complex / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D046911:Macromolecular Substances; D008565:Membrane Proteins / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013816:Thermodynamics
D000936:Antigen-Antibody Complex; D004791:Enzyme Inhibitors; D046911:Macromolecular Substances; D008565:Membrane Proteins; D011506:Proteins