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Symmetry 2018, 10(1), 25; doi:10.3390/sym10010025

A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models

1
Bioinformatics Division, Indian Institute of Information Technology, Allahabad 211012, India
2
CMBI, Radboud University Nijmegen Medical Centre, 6525 GA 26-28 Nijmegen, The Netherlands
Present address: Institute for Computer Science and Department of Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
*
Author to whom correspondence should be addressed.
Received: 20 November 2017 / Revised: 2 January 2018 / Accepted: 2 January 2018 / Published: 11 January 2018
(This article belongs to the Special Issue Structural Symmetry and Protein Function)
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Abstract

It is much easier to determine a protein’s sequence than to determine its three dimensional structure and consequently homology modeling will be an essential aspect of most studies that require 3D protein structure data. Homology modeling templates tend to be PDB files. About 88% of all protein structures in the PDB have been determined with X-ray crystallography, and thus are based on crystals that by necessity hold non-natural packing contacts in accordance with the crystal symmetry. Active site residues, residues involved in intermolecular interactions, residues that get post-translationally modified, or other sites of interest, normally are located at the protein surface so that it is particularly important to correctly model surface-located residues. Unfortunately, surface residues are just those that suffer most from crystal packing artifacts. Our study of the influence of crystal packing artifacts on the quality of homology models reveals that this influence is much larger than generally assumed, and that the evaluation of the quality of homology models should properly account for these artifacts. View Full-Text
Keywords: homology modeling; symmetry contact; side chain rotamericity homology modeling; symmetry contact; side chain rotamericity
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Singh, D.; Berntsen, K.R.M.; Baakman, C.; Vriend, G.; Lahiri, T. A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models. Symmetry 2018, 10, 25.

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