title: PROSESS: a protein structure evaluation suite and server.
abstract: PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy or computational modeling. While many structure evaluation packages have been developed over the past 20 years, PROSESS is unique in its comprehensiveness, its capacity to evaluate X-ray, NMR and predicted structures as well as its ability to evaluate a variety of experimental NMR data. PROSESS integrates a variety of previously developed, well-known and thoroughly tested methods to evaluate both global and residue specific: (i) covalent and geometric quality; (ii) non-bonded/packing quality; (iii) torsion angle quality; (iv) chemical shift quality and (v) NOE quality. In particular, PROSESS uses VADAR for coordinate, packing, H-bond, secondary structure and geometric analysis, GeNMR for calculating folding, threading and solvent energetics, ShiftX for calculating chemical shift correlations, RCI for correlating structure mobility to chemical shift and PREDITOR for calculating torsion angle-chemical shifts agreement. PROSESS also incorporates several other programs including MolProbity to assess atomic clashes, Xplor-NIH to identify and quantify NOE restraint violations and NAMD to assess structure energetics. PROSESS produces detailed tables, explanations, structural images and graphs that summarize the results and compare them to values observed in high-quality or high-resolution protein structures. Using a simplified red-amber-green coloring scheme PROSESS also alerts users about both general and residue-specific structural problems. PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at http://www.prosess.ca.
authors.affiliation: Department of Computing Science, University of Alberta, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Berjanskii
authors.forename: Yongjie
authors.initials: Y
authors.lastname: Liang
authors.forename: Jianjun
authors.initials: J
authors.lastname: Zhou
authors.forename: Peter
authors.initials: P
authors.lastname: Tang
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.forename: You
authors.initials: Y
authors.lastname: Zhou
authors.forename: Joseph
authors.initials: J
authors.lastname: Cruz
authors.forename: Cam
authors.initials: C
authors.lastname: MacDonell
authors.forename: Guohui
authors.initials: G
authors.lastname: Lin
authors.forename: Paul
authors.initials: P
authors.lastname: Lu
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
mesh_terms: D018360:Crystallography, X-Ray; D020407:Internet; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D012984:Software; D014584:User-Computer Interface
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W670-7
references.pmid: 19406927
references.citation: Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):829-32
references.pmid: 15299648
references.citation: J Mol Graph. 1996 Feb;14(1):51-5, 29-32
references.pmid: 8744573
references.citation: Nature. 1992 Mar 5;356(6364):83-5
references.pmid: 1538787
references.citation: EMBO J. 1986 Apr;5(4):823-6
references.pmid: 3709526
references.citation: J Mol Biol. 1996 Nov 22;264(1):121-36
references.pmid: 8950272
references.citation: Methods Mol Biol. 2004;278:353-78
references.pmid: 15318003
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502
references.pmid: 18515350
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W407-10
references.pmid: 17517781
references.citation: J Biomol NMR. 1996 Dec;8(4):477-86
references.pmid: 9008363
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W590-4
references.pmid: 15215457
references.citation: Acta Crystallogr D Biol Crystallogr. 2009 Feb;65(Pt 2):193-9
references.pmid: 19171975
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90
references.pmid: 18326625
references.citation: J Biomol NMR. 2008 Jan;40(1):31-48
references.pmid: 17985196
references.citation: J Mol Biol. 1999 Jan 29;285(4):1735-47
references.pmid: 9917408
references.citation: Nature. 1996 May 23;381(6580):272
references.pmid: 8692262
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3316-9
references.pmid: 12824316
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83
references.pmid: 17452350
references.citation: J Biomol NMR. 2003 Mar;25(3):173-95
references.pmid: 12652131
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W63-9
references.pmid: 16845087
references.citation: J Comput Chem. 2005 Dec;26(16):1781-802
references.pmid: 16222654
references.citation: J Biomol NMR. 2003 Jul;26(3):215-40
references.pmid: 12766419
references.citation: J Am Chem Soc. 2005 Feb 16;127(6):1665-74
references.pmid: 15701001
references.citation: Nature. 2007 Aug 9;448(7154):E1-2; discussion E2-3
references.pmid: 17687277
references.citation: J Magn Reson. 2003 Jan;160(1):65-73
references.pmid: 12565051