Classification of protein complexes based on docking difficulty.
Based on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein-protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the targets of the CAPRI docking experiment. Results show that targets with a moderate expected difficulty were indeed predicted well by a number of groups, whereas the use of additional a priori information was necessary to obtain good results for some very difficult targets. The analysis indicates that CAPRI and other relatively large-scale docking studies represent very important steps toward understanding the capabilities and limitations of current protein-protein docking methods.
Vajda
Sandor
S
Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA. vajda@bu.edu <vajda@bu.edu>
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D019281:Dimerization; D020407:Internet; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D040681:Structural Homology, Protein
D046911:Macromolecular Substances; D011506:Proteins