Automated minimization of steric clashes in protein structures

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Automated minimization of steric clashes in protein structures.

Molecular 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. Us...

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Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA against the endonuclease activity by methylation. It is widely believed that the methylated DNA would not 'fit' into the binding site of the endonuclease in the productive orientation, and thus steric clashes should account for most of the protection. We test this concept statistically by grafting met...

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ژورنال

عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics

سال: 2010

ISSN: 0887-3585

DOI: 10.1002/prot.22879