I also should have added that if you use a predicted structure and you run MR with it and then modify it to fit the data of your novel structure then, for sure, MolProbity applies or other tools as you will find in the various packages and on the PDB site.
The most current predicted structures usually do have an energy minimisation step at the end but nevertheless you can always add it yourself as Xavier pointed out. In general, your prediction is a very good, educated guess on what your protein might look like. However, the algorithm has no clue about your crystallisation condition or even the true biological environment in the cell and hence cannot take this chemical information into account when arranging the atoms. The algorithm also doesn't know that you have a membrane protein or different domains that need to be arranged relative to each other. The artefacts mentioned by Xavier are most likely a result for this lack of knowledge by the algorithm. Or just poor performance after all, even the best predictor can't do magic... Look at the pLDDT score for your prediction, a local measure for the confidence with which each residue was placed into 3D space. A low score (<50) means high uncertainty and these residues should be removed anyway. So, open your model in Coot, look at it and remove the rubbish... M ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of F.Xavier Gomis-Rüth <[email protected]> Sent: 21 December 2021 10:04 To: [email protected] <[email protected]> Subject: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction Dear all, this is by far not the general case in our hands. Depending on which AlphaFold protocol is used, the resulting models have locally disfavourable geometries–including clashes–, impossible chain crossovers, etc. I would definitively recommend everybody to go through the model in detail and perform a final geometry minimization with Coot and/or Phenix/Refmac. And in these cases, general geometry validation as provided by MolProbity provides a final proof of the computational model. Best, Xavier -------- Forwarded Message -------- Subject: Re: [ccp4bb] Validation of structure prediction Date: Tue, 21 Dec 2021 09:43:37 +0000 From: Vollmar, Melanie (DLSLtd,RAL,LSCI) <[email protected]><mailto:[email protected]> Reply-To: Vollmar, Melanie (DLSLtd,RAL,LSCI) <[email protected]><mailto:[email protected]> To: [email protected]<mailto:[email protected]> Tristan is spot on. All the predicted structures have near perfect geometry, so commonly used validation tools like MolProbity can no longer be applied. What you need to consider is biological relevance of the predicted model. Does the model correctly reflect residue arrangement in the active site? Are domains in correct relative orientation to allow for interactions and movements, perhaps found by some other assay? Is there appropriate room to fit a ligand/cofactor? Are transmembrane helices, if there are any, correctly found? You need to map the knowledge you have of your protein to the structure and see if the atom positions and what you know support each other. Cheers M ________________________________ From: CCP4 bulletin board <[email protected]><mailto:[email protected]> on behalf of Tristan Croll <[email protected]><mailto:[email protected]> Sent: 21 December 2021 08:28 To: [email protected]<mailto:[email protected]> <[email protected]><mailto:[email protected]> Subject: Re: [ccp4bb] Validation of structure prediction I agree with Dale. Tools like MolProbity are not the right approach to validating a structure prediction. To understand why, just consider that all you need to do to get a perfect MolProbity score is predict every structure as a single long alpha helix with ideal rotamers, with a kink at each proline. To validate a predicted structure will require a completely different toolset - one that I’m not sure fully exists yet. — Tristan > On 20 Dec 2021, at 18:47, Dale Tronrud > <[email protected]><mailto:[email protected]> wrote: > > I don't see any reason to believe that software designed to validate > crystallographic or NMR models would have any utility validating AlphaFold > predicted models. Doesn't the prediction software already ensure that all > the indicators used by Molprobity are obeyed? I'm afraid that the tools to > validate any new technique must be designed specifically for that technique. > (And when they become available they will be useless for validating > crystallographic models!) > > Dale E. Tronrud > >> On 12/20/2021 10:28 AM, Nicholas Clark wrote: >> The Molprobity server can be run online and only requires the coordinates in >> PDB format: http://molprobity.biochem.duke.edu/ >> <http://molprobity.biochem.duke.edu/>. >> Best, >> Nick Clark >> On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat >> <[email protected]<mailto:[email protected]> >> <mailto:[email protected]>> wrote: >> Hi, >> Can anyone suggest how to validate a predicted structure? Something >> similar to wwPDB validation without the need for refinement >> statistics. I realize this is a strange question given that the >> geometry of the model is anticipated to be fine if the structure was >> predicted by a server that minimizes the geometry to improve its >> statistics. Nonetheless, the journal has asked me for such a report. >> Thanks. >> Best wishes, >> Reza >> Reza Khayat, PhD >> Associate Professor >> City College of New York >> Department of Chemistry and Biochemistry >> New York, NY 10031 >> ------------------------------------------------------------------------ >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> -- >> Nicholas D. Clark >> PhD Candidate >> Malkowski Lab >> University at Buffalo >> Department of Structural Biology >> Jacob's School of Medicine & Biomedical Sciences >> 955 Main Street, RM 5130 >> Buffalo, NY 14203 >> Cell: 716-830-1908 >> ------------------------------------------------------------------------ >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions > are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ________________________________ 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 ######################################################################## 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/
