Homology modeling of membrane proteins: a critical assessment.
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.
Molecular Modelling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India.
Ch Surendhar
ChS
Reddy
K
K
Vijayasarathy
E
E
Srinivas
G Madhavi
GM
Sastry
G Narahari
GN
Sastry
D019295:Computational Biology; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software; D040681:Structural Homology, Protein
D008565:Membrane Proteins