NDLI: Computational Modelling of Protein Interactions: Energy Minimization for the Refinement and Scoring of Association Decoys

Content Provider	Springer Nature Link
Author	Dibrov, Alexander Myal, Yvonne Leygue, Etienne
Copyright Year	2009
Abstract	The prediction of protein–protein interactions based on independently obtained structural information for each interacting partner remains an important challenge in computational chemistry. Procedures where hypothetical interaction models (or decoys) are generated, then ranked using a biochemically relevant scoring function have been garnering interest as an avenue for addressing such challenges. The program PatchDock has been shown to produce reasonable decoys for modeling the association between pig alpha-amylase and the VH-domains of camelide antibody raised against it. We designed a biochemically relevant method by which PatchDock decoys could be ranked in order to separate near-native structures from false positives. Several thousand steps of energy minimization were used to simulate induced fit within the otherwise rigid decoys and to rank them. We applied a partial free energy function to rank each of the binding modes, improving discrimination between near-native structures and false positives. Sorting decoys according to strain energy increased the proportion of near-native decoys near the bottom of the ranked list. Additionally, we propose a novel method which utilizes regression analysis for the selection of minimization convergence criteria and provides approximation of the partial free energy function as the number of algorithmic steps approaches infinity.
Starting Page	419
Ending Page	428
Page Count	10
File Format	PDF
ISSN	00015342
Journal	Acta Biotheoretica
Volume Number	57
Issue Number	4
e-ISSN	15728358
Language	English
Publisher	Springer Netherlands
Publisher Date	2009-09-23
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Molecular mechanics Surface complementarity Protein–protein interactions GROMACS PatchDock Amylase Evolutionary Biology Philosophy of Biology
Content Type	Text
Resource Type	Article
Subject	Philosophy Applied Mathematics Medicine Biochemistry, Genetics and Molecular Biology Environmental Science Agricultural and Biological Sciences

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