[ccp4bb] Postdoc Position at Caltech

The Hoelz laboratory at the California Institute of Technology seeks to recruit an outstanding postdoctoral scientists in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. Thi

Re: [ccp4bb] Validation of structure prediction

Hi Reza, If you think about it this way... Validation is making sure that the model makes sense, data make sense and model-to-data fit make sense, then the answer to your question is obvious: in your case you do not have experimental data (at least in a way we used to think of it) and so then of t

Re: [ccp4bb] Validation of structure prediction

Hello, I think it is perfectly "valid" to run AlphaFold2 / RosettaFold / etc. models through geometry validation servers (aside from reporting their intrinsic quality indicators like TM-score and pLDDT distribution, as mentioned above by Randy Read). Since most experimental structures have a small

Re: [ccp4bb] Validation of structure prediction

Hi, Thank you for the help. I've addressed some of the concerns raised here in another thread. "Validation" referred to checking geometric parameters; however, outstanding geometric parameters do not indicate a structure that is comparable to an experimentally determined structure. The structu

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

​Dear all, Thank you for the responses. My question regarding validation was not directed at weather the prediction was correct (i.e. sufficiently comparable to the experimentally determined structure). I realize this question in itself is not easily answered. I also agree with what everyone h

Re: [ccp4bb] Validation of structure prediction

There are also dedicated homology modelling validation tools such as ANOLEA (ANOLEA (Atomic Non-Local Environment Assessment) (melolab.org)). Best wishes James From: CCP4 bulletin board on behalf of Nicholas Clark Sent: Tuesday, Dec

Re: [ccp4bb] Validation of structure prediction

Reza, Thus far, it seems we’ve all assumed this was an AlphaFold or RobettaFold model. If this is not indeed the case, it may be worthwhile to “validate” your mode by running your sequence through one of these two and using the validation from them. The AlphaFold DB can be found here, with a numb

Re: [ccp4bb] Validation of structure prediction

Just to add one point that I don’t think I’ve seen yet. If what the referee wants is a data-free assessment of the expected quality of the model, I think that the best assessment at the moment is the one done by AlphaFold2 (or indeed RoseTTAFold if you’re using one of their models). The machine-

Re: [ccp4bb] Validation of structure prediction

Hi Reza, the term "validation" as used by e.g. crystallographers - namely by checking geometric parameters of a structure derived from experiment(s) - is euphemistic since realistic geometry is a required but not sufficient property of a model - it can be completely wrong even if it has good ge

Re: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

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

[ccp4bb] Post-doctoral positions in GPCR biology at IIT Kanpur

Dear All, We have multiple, fully-funded post-doctoral positions available in our laboratory at the Indian Institute of Technology, Kanpur to work on cutting edge research projects related to GPCR biology including structural studies using cryo-EM, discovering novel signaling pathways using prote

[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 a

Re: [ccp4bb] Validation of structure prediction

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 si

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 pr