Automated minimization of steric clashes in protein structures

Srinivas Ramachandran; Pradeep Kota; Feng Ding; Nikolay V. Dokholyan

doi:10.1002/prot.22879

journal article Nov 05, 2010

Automated minimization of steric clashes in protein structures

Srinivas Ramachandran Pradeep Kota

Feng Ding

Nikolay V. Dokholyan

Proteins: Structure, Function, and Bioinformatics Vol. 79 No. 1 pp. 261-270 · Wiley

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Abstract

AbstractMolecular modeling of proteins including homology modeling, structure determination, and knowledge‐based protein design requires tools to evaluate and refine three‐dimensional protein structures. Steric clash is one of the artifacts prevalent in low‐resolution structures and homology models. Steric clashes arise due to the unnatural overlap of any two nonbonding atoms in a protein structure. Usually, removal of severe steric clashes in some structures is challenging since many existing refinement programs do not accept structures with severe steric clashes. Here, we present a quantitative approach of identifying steric clashes in proteins by defining clashes based on the Van der Waals repulsion energy of the clashing atoms. We also define a metric for quantitative estimation of the severity of clashes in proteins by performing statistical analysis of clashes in high‐resolution protein structures. We describe a rapid, automated, and robust protocol, Chiron, which efficiently resolves severe clashes in low‐resolution structures and homology models with minimal perturbation in the protein backbone. Benchmark studies highlight the efficiency and robustness of Chiron compared with other widely used methods. We provide Chiron as an automated web server to evaluate and resolve clashes in protein structures that can be further used for more accurate protein design. Proteins 2010. © 2010 Wiley‐Liss, Inc.

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Details

Published: Nov 05, 2010
Vol/Issue: 79(1)
Pages: 261-270
License: View

Authors

S

Srinivas Ramachandran

Department of Biochemistry and Biophysics, School of Medicine, and ‡Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States

P

Pradeep Kota

Department of Pharmacology and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States, and Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States

University of Virginia

Cite This Article

Srinivas Ramachandran, Pradeep Kota, Feng Ding, et al. (2010). Automated minimization of steric clashes in protein structures. Proteins: Structure, Function, and Bioinformatics, 79(1), 261-270. https://doi.org/10.1002/prot.22879

Automated minimization of steric clashes in protein structures

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