[ccp4bb] new PhD project

Dear all I'd be very happy if you made any suitable students aware of this new (fully-funded) PhD project at the intersection of structural bioinformatics and crystallography https://www.findaphd.com/phds/project/bbsrc-nwd-leveraging-deep-learning-based-structural-bioinformatics-for-experimenta

Re: [ccp4bb] cryoEM molecular replacement

Hi all Slice'N'Dice is another option for this. It will take a structure eg an AF2 prediction, remove low-confidence portions, and split the remainder using a variety of algorithms, including based on the PAE where that is available. Originally developed for MR (https://www.biorxiv.org/conten

[ccp4bb] PDRA position available for structure validation and MR software development at the University of Liverpool

[with apologies if you get this more than once] Dear all A 3-year position is available to develop software for structure validation using Deep Learning-derived predicted residue contacts and distances, and for optimal Molecular Replacement using the results of the latest RNA structure predict

[ccp4bb] PDRA positions available for CCP4 methods and software development

Please do not reply directly to this message CCP4 collaboratively develops and supports cutting edge methods for the experimental determination and analysis of protein structure, principally by X-ray crystallography. New developments are released through the CCP4 suite of programs, which includ

Re: [ccp4bb] Tools for structure-based multiple sequence alignment

Dear Manoj I would recommend CCP4's own GESAMT for this. Dan Sent from Outlook for Android From: CCP4 bulletin board on behalf of Manoj N Sent: Thursday, March 2, 2023 7:45:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Tools for st

Re: [ccp4bb] ContaMiner server down?

Dear Julian I don't know about ContaMiner, but you might also try SIMBAD for contaminant detection https://simbad.readthedocs.io/en/latest/ It's available at the command line, through i2 and Cloud interfaces, and at the CCP4 Online server https://ccp4online.ccp4.ac.uk/ccp4online/ Dan Pr

[ccp4bb] Fully funded PhD studentship: extended deadline

Dear all We have decided to extend the deadline on our new fully-funded PhD studentship. It's co-funded and co-led by Liverpool and CCP-EM and is a really exciting opportunity for the right student. Further details here https://www.findaphd.com/phds/project/efficient-matching-of-protein-structur

Re: [ccp4bb] looking for proteins with no homologues in pdb

One short cut would be to focus on Pfam families that do not yet have a 3D representative. They can be browsed eg https://pfam.xfam.org/family/browse?browse=a or you can also install Pfam locally as MySQL for programmatic access. Choosing Families rather than Domains would make it easier to ge

[ccp4bb] Fully-funded PhD at the University of Liverpool

Please pass on this information to any plausible candidates you know. Thanks Title: Efficient matching of protein structures to cryo-EM map segments Initial deadline: June 30th This project

Re: [ccp4bb] CCP4BB vs COVID19

Hi James 5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold similar to ORF7 (for which there is a structure; 1xak). https://toolkit.tuebingen.mpg.de/jobs/2717885_1 I must say I got quite excited seei

Re: [ccp4bb] Searching similar local structural conformations

Dear Lei You can use ASSAM for this http://27.126.156.175/assam/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394286/ In the past I've also used SPASM locally for this http://xray.bmc.uu.se/usf/spasm.html but I think you'll need to generate your own up to date database to search. Best wi

[ccp4bb] Joint Liverpool/Diamond PhD studentship

Dear all, A fully-funded 4-year PhD studentship, joint between the University of Liverpool and the Diamond Light Source, is now available. Paying an enhanced stipend, it involves application of computational methods to characterise and solve diffraction datasets from crystals of transmembrane h