Developing algorithms for predicting protein-protein interactions of homology modeled proteins.

Technical Report · Sun Jan 01 04:00:00 EST 2006

DOI:https://doi.org/10.2172/883467· OSTI ID:883467

Martin, Shawn Bryan; Sale, Kenneth L; Faulon, Jean-Loup Michel; Roe, Diana C

The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to predict theses interaction site. The second approach is to improve validation of predicted complexes after docking, and uses an improved scoring function for evaluating proposed docked poses, incorporating a solvation term. This scoring function demonstrates significant improvement over current state-of-the art functions. Initial studies on both these approaches are promising, and argue for full development of these algorithms.

• Research Organization: Sandia National Laboratories
• Sponsoring Organization: USDOE
• DOE Contract Number: AC04-94AL85000
• OSTI ID: 883467
• Report Number(s): SAND2005-7984
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ALGORITHMS
Homology theory.
PROTEINS
Protein Binding.
Protein folding-Computer simulation.
SOLVATION
VALIDATION