title: ProTSAV: A protein tertiary structure analysis and validation server.
abstract: Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality assessment of predicted model structures directs further research on function. Here we present a new server ProTSAV, capable of evaluating predicted model structures based on some popular online servers and standalone tools. ProTSAV furnishes the user with a single quality score in case of individual protein structure along with a graphical representation and ranking in case of multiple protein structure assessment. The server is validated on ~64,446 protein structures including experimental structures from RCSB and predicted model structures for CASP targets and from public decoy sets. ProTSAV succeeds in predicting quality of protein structures with a specificity of 100% and a sensitivity of 98% on experimentally solved structures and achieves a specificity of 88%and a sensitivity of 91% on predicted protein structures of CASP11 targets under 2Å.The server overcomes the limitations of any single server/method and is seen to be robust in helping in quality assessment. ProTSAV is freely available at http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp.
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi, India; Department of Bioinformatics, Banasthali Vidyapith, Banasthali, 304022, India.
authors.forename: Ankita
authors.initials: A
authors.lastname: Singh
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi, India; Kusuma School of Biological Sciences, IIT Delhi, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Kaushik
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi, India; Kusuma School of Biological Sciences, IIT Delhi, India.
authors.forename: Avinash
authors.initials: A
authors.lastname: Mishra
authors.affiliation: Department of Bioinformatics, Banasthali Vidyapith, Banasthali, 304022, India.
authors.forename: Asheesh
authors.initials: A
authors.lastname: Shanker
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi, India; Kusuma School of Biological Sciences, IIT Delhi, India; Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India. Electronic address: bjayaram@scfbio-iitd.res.in.
authors.forename: B
authors.initials: B
authors.lastname: Jayaram
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D012986:Software Validation
chemical_list: D011506:Proteins
keywords: Protein structure quality assessment; Structure evaluation; Structure validation