Evaluation of geometric complementarity between molecular surfaces using compactly supported radial basis functions.
One of the challenges faced by all molecular docking algorithms is that of being able to discriminate between correct results and false positives obtained in the simulations. The scoring or energetic function is the one that must fulfill this task. Several scoring functions have been developed and new methodologies are still under development. In this paper, we have employed the Compactly Supported Radial Basis Functions (CSRBF) to create analytical representations of molecular surfaces, which are then included as key components of a new scoring function for molecular docking. The method proposed here achieves a better ranking of the solutions produced by the program DOCK, as compared with the ranking done by its native contact scoring function. Our new analytical scoring function based on CSRBF can be easily included in different available docking programs as a reliable and quick filter in large-scale docking simulations.
Diago
Luis A
LA
Department of Mechanical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguroku, PO Box 152-8550, Tokyo, Japan. diago.l.aa@m.titech.ac.jp
Moreno
Ernesto
E
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D013499:Surface Properties
D008024:Ligands