Re: [ccp4bb] PDB to AlphaFold via Uniprot

Or you can go straight to uniprot. Every available PDB + alphafold model is linked to the uniprot entry. On Fri, Jul 29, 2022 at 4:46 PM Robbie Joosten wrote: > Hi Paul, > > From the PDB file get the Uniprot primary accession code (see DBREF) and > use this to get the Alphafold model using 3D-b

[ccp4bb] Structural Biologist opening at H3 Biomedicine (Cambridge - USA)

Hi All, We have an exciting job opportunity in structural biology! *Please apply at:* https://us.eisai.com/careers-at-eisai/job-detail?searchParam=H3%20Biomedicine&id=JOB_POSTING-3-9560 H3 is an oncology-focused company leveraging the latest cancer genomics data to inform drug discovery. The qua

Re: [ccp4bb] Bug in mmCIF handling of UNK residues?

I hope this doesn't confuse the discussion, but my understanding was "UNK" stood for "unknown" residue and this will cause errors. UNK naming convention is the default output of Schrodinger when generating ligand PDB files. Coot will display the PDB containing "UNK" as a residue, but if you try t

Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

Hi Frank, I thought we were working quickly, but we only just got all of your structures uploaded in our Proasis system today and can only now begin analysis and design ideas. I don't know if we will have much of anything by your deadline. Will there be additional design rounds? Thanks again for

Re: [ccp4bb] COVID-19 - help design protease inhibitors - 1st round Thurs midnight

Hi Frank, Congratulations on this impressive and valuable contribution to the efforts against covid and I applaud your transparency and crowdsourcing efforts on this global problem. Your team is really an inspiration to us all. We are working to get all your structures uploaded for our med chemis

[ccp4bb] company data base

Dear CCP4 users, This is off topic and directed more towards industry users. I would really appreciate any help recommending an in house "PDB" data base for storing proprietary structures. My impression is the big pharma make their own customized data base and a lot of biotechs just dump their co

[ccp4bb] Structure biologist opening at H3 Biomedicine (Cambridge, USA)

Dear All, we have an opening for a permanent hire in my group so please send me your resumes if interested and/or please forward to anyone you know who may be looking for a terrific opportunity in biotech. Thanks! Nick *Scientist – Structural Biology* *Contact: nicholas_lar...@h3biomedicine.co

[ccp4bb] HDX data representation

Dear Colleagues, We recently acquired HDX data on a target, which basically gives us %change per residue over the entire primary sequence. Is there a simple way to reassign the B-factor column of my PDB with those %change numbers so I can then easily color the molecular surface? I hope the questi

Re: [ccp4bb] PDB based Fold recognition

You use the Dali server for that :) http://ekhidna.biocenter.helsinki.fi/dali_server On Mon, Sep 18, 2017 at 12:21 PM, Chetan Arya wrote: > Hi all, > I want to know if there is any server/software which does the PDB based > (structure based) fold recognition. All I got for fold prediction are

Re: [ccp4bb] Protein rapidly precipitates when off ice

Did anyone suggest adding any known ligand? If your protein happens to bind some compound/peptide/DNA/RNA/whatever, including that other partner could dramatically change it's solution properties and be an easy fix for your handling/formulation issues. Good luck! On Fri, Jul 14, 2017 at 6:33 AM,

Re: [ccp4bb] off-topic: negative thermal shift upon ligand binding

In theory, what you say is quite sensible. But there is one interesting counter example I am aware of.The fragment tool compound that eventually gave rise to the clinical compound indeglitazar ( http://www.pnas.org/content/106/1/262.full.pdf) gives a negative shift by DSF (in our hands): [imag

Re: [ccp4bb] Large number of outliers in the dataset

One thing that sometimes helps me in this situation is reprocess and refine in lower symmetry like P21. It could be you have pseudosymmetry and need to model more molecules in the AU to better reflect your data. Sometimes this can help. If that doesn't work, then you may have to stick with your

[ccp4bb] ITC question

Dear colleagues, We have a target where people have measured Kd's for ligands using radioligand binding assays. Several publications report Kd's of single digit nanomolar and we are able to reproduce that data using this assay format. When we try to do the same measurement using ITC, we generate

Re: [ccp4bb] AW: [ccp4bb] Composit omit map vs. ligand

I agree with Herman about shorter soak. In addition, if your crystals can tolerate any change in pH, you can slow your reaction down by tweaking this parameter. Another thing you should think about is the kinetics of the reaction, especially the rate limiting step. If the rate limiting step is p

Re: [ccp4bb] How to determine the concentration of biotinylated peptide?

These suggestions are all possible, but why not simply lyophilize it into a tared tube and weigh it out? On Mon, Feb 6, 2017 at 12:28 PM, Alex Lee wrote: > Thank you all for your suggestions! > > On Mon, Feb 6, 2017 at 5:53 AM, Artem Evdokimov > wrote: > >> Hi, >> >> In addition to HABA dye ass

[ccp4bb] Glass etching of structure

Dear All, I'm sorry if this is off topic, but it might be of interest to general audience. I want to get one of our crystal structures etched in glass. Can anyone help recommend a company that can provide this service? BioEtch had come highly recommended to me, but unfortunately their website cur

[ccp4bb] jligand help

Dear All, I have CCP4 6.5.0 installed on my laptop PC. Everything runs fine, to my knowledge, except JLigand. When I click this program from the program list, absolutely nothing happens. No error message, nothing. It doesn't launch. Do I need to reinstall cpp4 or is JLigand a separate installa

Re: [ccp4bb] The phase problem

Screen for heavy atoms with native gel. Run protein with variety of heavy atoms. If you see a discreet shift in the native gel, then you will get derivative. If you don't see a shift, don't bother soaking. It's worked for me every time. Also, ammonium sulfate will mess up your heavy atoms, so

[ccp4bb] KRAS maps

Dear All, I frequently use the Coot feature "Fetch PDB and MAP using EDS..." with great success when peer reviewing literature reports. However, when I try this for the recent KRAS structures deposited by Kevan Shokat and Jim Wells (Nature 2013), the Coot generated maps are garbage, although the r

Re: [ccp4bb] How to store PEG screens

I don't think storage matters. I doubt Hampton stores their PEG stock solutions at -80 before they ship out to customers. I've solved tons of structures leaving my PEGS and PEG screens at RT in the light. Nick On Mon, Jul 14, 2014 at 12:32 PM, Chris Fage wrote: > Hi Jerome, > > -I have heard

Re: [ccp4bb] Unidentified density in coot

Looks like you're on the twofold axis, which will make interpretation challenging. Anything you put in may end up being too close to itself in the neighboring AU. What happens if you put in a water and display the symmetry? On Mon, Jun 23, 2014 at 8:17 AM, Shanti Pal Gangwar wrote: > Dear All

[ccp4bb] Industry Postdoc Position - Boston

H3 Biomedicine seeks to recruit an outstanding postdoctoral candidate in structural biology. Our major area of research is RNA splicing in cancer. We have developed tool molecules targeting aberrant splicing in SF3B1 mutant cancers. Our goal is to understand the structural basis for aberrant splic