title: Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.
abstract: We propose a new computational approach for protein docking exploiting energy funnels in the 6-dimensional space of translations and rotations of the ligand with respect to the receptor. Our approach consists of a series of translational and orientational moves of the ligand towards the receptor. Each move is performed using a global optimization method we have developed - the semi-definite underestimation (SDU) method - which can exploit a funnel-like energy function. We compared our approach with Monte Carlo on a set of 10 protein complexes using two residue-level potentials. To achieve the same level of performance (produce a near-native < or =3 A RMSD complex) our approach reduces energy evaluations by more than a factor of two, on average.
authors.affiliation: Center for Information & Systems Eng., and Dept. of Manufacturing Eng., Boston University, Blookline, MA 2446, USA. yannisp@bu.edu
authors.forename: Ioannis Ch
authors.initials: ICh
authors.lastname: Paschalidis
authors.forename: Yang
authors.initials: Y
authors.lastname: Shen
authors.forename: Pirooz
authors.initials: P
authors.lastname: Vakili
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
mesh_terms: D000465:Algorithms; D002468:Cell Physiological Phenomena; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D008024:Ligands; D008958:Models, Molecular; D008962:Models, Theoretical; D009010:Monte Carlo Method; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins