Dear Amit, I don’t think that PROCHECK is the right tool for assessing the quality of a comparative model. It was revolutionary in its time, but the criteria it looks at can mostly be satisfied by energy minimisation even of an incorrect model, especially if you don’t have to simultaneously satisfy experimental data. For evaluating refined experimental models, I would now be inclined to use Molprobity (available from a website, CCP4 and Phenix) or tools built into graphics programs like ISOLDE and coot.
Model quality assessment is actually a thriving subfield in the protein modeling community and it has its own category in the CASP modeling challenges. You want to be looking at the methods that have been judged best by seeing how well they perform in blind predictions. Comparative models differ from experimental models in that they haven’t been constrained by the requirement to fit experimental data, so quality assessment has to look at more subtle features like residue environment. The most recent CASP was CASP13, so a good start would be the main model quality assessment evaluation in the special issue from that event: https://onlinelibrary.wiley.com/doi/10.1002/prot.25767. You’ll find a variety of good tools described there. The one we’ve been playing with, in terms of local assessment of model quality for MR, is ProQ3D, which has an online server: http://proq3.bioinfo.se. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 15 Aug 2020, at 00:39, amit gaur <cdriamitg...@gmail.com> wrote: > > Hi All, > I am trying to generate a model using comparative modeling. Can anybody > suggest the quality of the model based on procheck summary. > > +----------<<< P R O C H E C K S U M M A R Y > >>>----------+ > | > | > | /var/www/PROCHECK/Jobs/7358861/7358861.pdb 1.5 1253 residues > | > | > | > *| Ramachandran plot: 87.9% core 10.2% allow 1.4% gener 0.4% disall > | > | > | > *| All Ramachandrans: 67 labelled residues (out of1235) > | > +| Chi1-chi2 plots: 3 labelled residues (out of 771) > | > | Side-chain params: 5 better 0 inside 0 worse > | > | > | > *| Residue properties: Max.deviation: 4.9 Bad contacts: 0 > | > *| Bond len/angle: 9.9 Morris et al class: 1 1 2 > | > | > | > | G-factors Dihedrals: -0.13 Covalent: -0.07 Overall: -0.10 > | > | > | > *| Planar groups: 90.0% within limits 10.0% highlighted 13 off graph > | > | > | > > +----------------------------------------------------------------------------+ > + May be worth investigating further. * Worth investigating further. > > > > Thanks, > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
