Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

BMC Bioinformatics

Research

Goutam Mukherjee¹  Priyanka Dhingra¹  B Jayaram²  Shashank Shekhar³  Ankita Singh³  Rahul Kaushik⁴  Avinash Mishra⁴ 

[1] Department of Chemistry, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Department of Chemistry, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, 110016, New Delhi, India;

关键词: Protein tertiary structure prediction;    ab initio;    homology;    RMSD;    protein folding;   

DOI  :  10.1186/1471-2105-15-S16-S7

来源: Springer

【 摘 要 】

BackgroundThe advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals.ResultsBhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥0.5 in 91% of the cases and Cα RMSDs ≤5Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution.ConclusionBhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment.

【 授权许可】

CC BY   
© Jayaram et al.; licensee BioMed Central Ltd. 2014