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Homology modeling of membrane proteins: A critical assessment

Paper ID Volume ID Publish Year Pages File Format Full-Text
15505 1419 2006 7 PDF Available
Title
Homology modeling of membrane proteins: A critical assessment
Abstract

Evaluation and validation of homology modeling protocols are indispensable for membrane proteins as experimental determination of their three-dimensional structure is an arduous task. The prediction ability of Modeller, MOE, InsightII-Homology and Swiss-PdbViewer (SPV) with different sequence alignments CLUSTALW, BLAST and 3D-JIGSAW have been assessed. The sequence identity of the target and template was chosen to be in the range of 25–35%. Validation protocols to assess the structure, fold and stereochemical quality, are employed by comparing with experimental structures. Two different ranking schemes are suggested to evaluate the performance of each methodology based on the validation scores. While unambiguous preference for any given procedure did not surface, statistically Modeller and the sequence alignment technique, 3D-JIGSAW, gave best results amongst the chosen protocols. The present study helps in selecting the right protocols when modeling membrane proteins, which form a major class of drug targets.

Keywords
Membrane proteins; 3-Dimensional structure; Homology modeling; Low sequence identity; Stereochemical quality; Structural similarity; Fold
First Page Preview
Homology modeling of membrane proteins: A critical assessment
Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 30, Issue 2, April 2006, Pages 120–126
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering