[ccp4bb] Fwd: [ccpem] Glutamate receptor cryo-EM at the MRC LMB

Hi everyone, I’m forwarding this position in structural biology and drug development at the LMB in Cambridge with my former PhD supervisor, Ingo Greger, in collaboration w AstraZeneca in case anyone is interested who is not on CCPEM. It’s a very dynamic, interdisciplinary group that I highly

Re: [ccp4bb] biomolecular NMR for IDPs

It is possible to get an ensemble for an intrinsically disordered segment from NMR. We did this in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008819/ Best wishes James On Aug 15, 2021, at 14:48, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: Hello, my numpty-level

Re: [ccp4bb] biomolecular NMR for IDPs

imagine. I suggest you get in touch with someone who actually does NMR. I just wanted to let you know that this is potentially possible. Best wishes James From: Sorin Draga Sent: Sunday, August 15, 2021 3:03 PM To: Krieger, James M Cc: CCP4BB@JISCMAIL.AC.UK Subject

Re: [ccp4bb] biomolecular NMR for IDPs

Dear Harry, Thanks very much for the info about RoseTTAFold. As for AlphaFold, there are ways to run it through Google Colab e.g. https://t.co/kxvjLVFwQx I’d also advise against using these for IDPs. Best wishes James On Aug 17, 2021, at 17:13, Harry Powell - CCP4BB

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,

Re: [ccp4bb] viral protein BLAST

PSI-BLAST (position specific iterative BLAST I think it stands for) and other BLAST variants may help - there are quite a few on NCBI now. There are also some other nice tools such as HHPred at https://toolkit.tuebingen.mpg.de/. Maybe HMMer could be a good option too. I’m not sure if any of

Re: [ccp4bb] ligand binds to one molecule

Perhaps the subunits have different conformational states that are differently able to bind the ligand. There are definitely oligomers where the subunits do that e.g. mGluR1 binding domain dimer is usually 1 open subunit and 1 closed in the active state without cations at the interface. This is

Re: [ccp4bb] Help with interpreting Tyrosine modification

Probably arginine and tyrosine do like each other a fair bit. They can form both cation-pi interactions and hydrogen bonds. Best wishes James On 1 Feb 2022, at 16:41, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: Hello, I did wonder if it might be an alternative

Re: [ccp4bb] PDB deposition of structure solved with a Robetta model

What do people think about depositing the Robetta model to somewhere like Zenodo (or maybe PDB-Dev) and getting an id from that? Best wishes James On 7 Feb 2022, at 13:25, Loll, Bernhard wrote: Dear all, I have recently solved a structure by molecular replacement with a search model

Re: [ccp4bb] Easy/Silly question

Oh, yes. Sorry. From: Robbie Joosten Sent: Friday, July 1, 2022 10:02 AM To: Krieger, James M ; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Easy/Silly question BMA is mannose, not maltose > -Original Message- > From: CCP4 bulletin board On

Re: [ccp4bb] Easy/Silly question

How about BMA for beta-D-maltose? On 1 Jul 2022, at 05:55, Nigel Moriarty wrote:  Yes, MAL was obsoleted about 2 years ago. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone

Re: [ccp4bb] Regarding Protein biological assembly

Hi Abhilash, You should also be able to do this with the ProDy python package. Once installed open a python terminal and type the following: from prody import * biomols = parsePDB(list_of_ids, biomol=True, extend_biomol=True) # this will take files in whichever format is available for b in

Re: [ccp4bb] Regarding Amber Force field

Hello! It’s probably better to ask CCPBioSim rather than ccp4 for this kind of question as many people there will not be here too. I’ve tried adding their mailing list here. What are you trying to do and why do you need amber99 and what’s wrong with the one in gromacs? It looks like the AMBER

Re: [ccp4bb] Adding metal ions

Charmm-gui can add copper ions and lots of other ones. They seem to have removed the option of adding specific ions by numbers and instead give a box for concentration and an option to check how many there are. This depends a lot on the size of the box around the protein and you can maybe do a

Re: [ccp4bb] Calculation of energetics for many mutations

Hi Nick, This would probably be a better question for the CCPBioSim mailing list: ccpbio...@jiscmail.ac.uk There are several free energy simulation methods including alchemical ones that may help with mutations. Perhaps some docking-based approaches may be useful too. Best wishes James

Re: [ccp4bb] RMSF calculation in pymol

I don’t have one for pymol, but there is a function in prody for it. Best wishes James On 14 Dec 2023, at 21:41, Srivastava, Dhiraj wrote:  Hi All sorry for off topic question. does anyone have script for rmsf calculation of multistate pdb file in pymol? There used to be a

Re: [ccp4bb] Can ALF3OH mimic the transition state?

There is also discussion about this for chaperonins such as CCT and GroEL. It may be that beryllium fluoride works better. Best wishes James > On 12 Dec 2023, at 05:30, Matthew BOWLER wrote: > > Dear Jinyu, > we observed exactly this in PGK - see https://doi.org/10.1021/ja100974t where > we

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hi Robbie and everyone, Perhaps some clustering of the structure could be used to define TLS groups rather than using chains. A spectral clustering based on Gaussian network model normal modes seems to work fairly well for defining dynamical domains, for example. In some cases these may be

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

It definitely is impressive but it also has clear limitations On 13 May 2024, at 15:22, Sylvia Fanucchi wrote:  You don't often get email from d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. Learn why this is