A quality metric for homology modeling: the H-factor

BMC Bioinformatics

Research Article

Patrice Koehl¹  Eric di Luccio² 

[1] Computer Science Department, Room 4337, Genome Center, GBSF University of California Davis, 451 East Health Sciences Drive, 95616, Davis, CA, USA;Computer Science Department, Room 4337, Genome Center, GBSF University of California Davis, 451 East Health Sciences Drive, 95616, Davis, CA, USA;School of Applied Biosciences, Kyungpook National University (KNU), 1370 Sangyeok-dong, Buk-gu, 702-701, Daegu, Republic of Korea;

关键词: Nuclear Magnetic Resonance;    Protein Data Bank;    Homology Modeling;    Nuclear Magnetic Resonance Spectroscopy;    Nuclear Magnetic Resonance Structure;   

DOI  :  10.1186/1471-2105-12-48

 received in 2010-08-03, accepted in 2011-02-04,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cannot be solved experimentally for technical or sometimes simply for time constraints, in silico protein structure prediction is expected to step in and generate a more complete picture of the protein structure universe. Molecular modeling of protein structures is a fast growing field and tremendous works have been done since the publication of the very first model. The growth of modeling techniques and more specifically of those that rely on the existing experimental knowledge of protein structures is intimately linked to the developments of high resolution, experimental techniques such as NMR, X-ray crystallography and electron microscopy. This strong connection between experimental and in silico methods is however not devoid of criticisms and concerns among modelers as well as among experimentalists.ResultsIn this paper, we focus on homology-modeling and more specifically, we review how it is perceived by the structural biology community and what can be done to impress on the experimentalists that it can be a valuable resource to them. We review the common practices and provide a set of guidelines for building better models. For that purpose, we introduce the H-factor, a new indicator for assessing the quality of homology models, mimicking the R-factor in X-ray crystallography. The methods for computing the H-factor is fully described and validated on a series of test cases.ConclusionsWe have developed a web service for computing the H-factor for models of a protein structure. This service is freely accessible at http://koehllab.genomecenter.ucdavis.edu/toolkit/h-factor.

【 授权许可】

CC BY   
© di Luccio and Koehl; licensee BioMed Central Ltd. 2011