Work

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels

Year: 2006

Type: conference-paper

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.

Source: Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

DOI: 10.1109/iembs.2006.260790

Authors: Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda

Institution: Boston University

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Institute of General Medical Sciences

Awards: G2247940252, A multistage approach to protein-protein docking, Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ, Final-Stage Optimization Methods for Protein Docking Exploiting Energy Funnels, G700947639