[ccp4bb] CryoEM current practices webinar - this week

Dear all, Please join the NIH supported CryoEM centers this Thursday for our June installment of the monthly CryoEM Current Practices webinar. When: Thursday, June 27, 2024 at 9 AM pacific / 12 PM eastern time Speaker: Dr. Keerthi Gottipati, Indiana University, Bloomington Title: Cryo-EM struct

Re: [ccp4bb] List of 3-letter codes of modified amino acids

Yes, having recently gone through most of the protein modification data currently in the archive, the PDB biocurators have overall been very consistent with the handling of protein modifications. Despite this, inconsistencies have accumulated over the years. In the current project, we are addin

Re: [ccp4bb] List of 3-letter codes of modified amino acids

For those who do not know, I worked on data processing for the PDB from 1974 to 1998 (entries 15 to ~9000) and we tried to be consistent in representing small modifications to amino acids: modified amino acid vs. standard amino acid plus het group. With the then lack of software tools we strug

Re: [ccp4bb] List of 3-letter codes of modified amino acids

Hi Frances, This is one of the central issues being addressed as part of the protein modifications project. When the PDB archive is updated as part of the project rollout, all protein modifications will be grouped into distinct categories of modification. The category they fall in determines

Re: [ccp4bb] List of 3-letter codes of modified amino acids

Would it be possible for the PDB to explain the distinction in representation between the case of a modified amino acid and the case of additional atoms bound to the side chain of a standard amino acid. If it is a standard amino acid will the extra atom(s) always be represented as a het group?

Re: [ccp4bb] List of 3-letter codes of modified amino acids

Hi everyone, Last year wwPDB standardised the backbone atom names for all residues that are part of a polypeptide sequence within the PDB archive. A full list of all chemical components affected can be found at: github.com/wwPDB/backbone-extension/tree/master/data/ccds This is a list of all mo

Re: [ccp4bb] List of 3-letter codes of modified amino acids

Hi folks “Can of worms” is how this could be described! From various different sources (many thanks Paul, Mitch, Robbie) I have now managed to obtain (inter alia) lists of 31, 189, 863 and 916 modified amino acids - and there are other, longer (and possibly shorter and equimetric [is that even

[ccp4bb] Job opportunities at SARomics Biostructures

Dear all, I'd like to draw your attention to job opportunities at SARomics Biostructures in Lund, Sweden, a rapidly growing CRO in structural biology for the pharma and biotech sectors, based in Lund, Sweden. SARomics are looking to recruit several scientists in protein expression and purificat

Re: [ccp4bb] List of 3-letter codes of modified amino acids

Hi Harry, A BSc student in our lab just had a look at this. Here is the list of mappings pdb-redo uses: https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif (second to last loop). Cheers, Robb

[ccp4bb] List of 3-letter codes of modified amino acids

Hi An internet search doesn’t yield an obvious list of these (I did find a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included appears to be dead - http://deposit.pdb.org/hetdictionary.txt). I’m almost convinced that this has been asked here previously (if not r

Re: [ccp4bb] searching for ligands with double conformation

Dear Anat, Replying on behalf of Chris Thorpe: The only reliable way I've found is to compare the conformations in each of the biological units and also to look for ALTLOCs. Obviously you can automate all of this, using BioPandas to compare peptide conformations (looking at position level RMS

Re: [ccp4bb] Server to find structural similarity between nucleic acid structures

Dear Marc, I'm not sure if there are tools to find global similarity, but you can use tools like NASSAM (http://211.25.251.163/nassam/), WebFR3D (https://www.bgsu.edu/research/rna/web-applications/webfr3d.html) or RAG3D (http://www.biomath.nyu.edu/?q=RAG3D) to do substructure search. Kind re

[ccp4bb] searching for ligands with double conformation

Dear CCP4 community, I am interested in searching in the PDB for ligands that are in complex with proteins in the PDB that were deposited with a double conformation. Does anyone know how to run such a search? How to define it? Thanks a lot for your help, Anat. ==

[ccp4bb] Server to find structural similarity between nucleic acid structures

Hello, I am looking for a server that finds structural similarities between the structure of an RNA and all RNA structures present in the PDB, pretty much like DALI or PDB-eFold do for proteins. Does anyone know if such server exists? Thanks a loot for your help, Best wishes, Marc — Marc G

[ccp4bb] Projects for Undergraduate Research

Hello all, We are looking for some candidate proteins/project ideas for undergraduate research in biochemistry. Preferable proteins expressed and soluble in bacteria, simple enough to purify (affinity chromatography) , it will be nice to perform some simple biochemical characterization(binding ass

[ccp4bb] EMDB & EMPIAR are hiring

Dear community, This is just a reminder that there are two weeks left to apply for an exciting opening for a biocurator position within the EMDB and EMPIAR teams. You can apply your structural biology domain knowledge to our highly important and unique global mission to provide open-access to b