Re: [ccp4bb] Measuring angles between domains

Hi Kyle I have used this pymol plugin to measure the angle between domains https://pymolwiki.org/index.php/Angle_between_domains Regards Ishan On Sat, Nov 13, 2021, 12:35 AM Kyle Gregory < 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear CCP4 bulletin board, > > I have two domains

[ccp4bb] Measuring angles between domains

Dear CCP4 bulletin board, I have two domains connected by a helix and I want to measure tilt angles between domains, for comparison purposes to other structures of the same protein. Does anyone have any tools they'd recommend? Kind regards, Kyle #

[ccp4bb] Announcement 9th International BioXFEL Conference

Dear Colleagues, The NSF BioXFEL Science and Technology Center is pleased to announce our 9th Annual International Conference Feb 8-10, 2022 chaired by Tonya Kuhl, UC-Davis, and Thomas Grant, UB. Registration is now open. The meeting is currently virtual but we are investigating the potential

Re: [ccp4bb] High-order oligomers vs robust crystals - references?

One could use PISA to get a rough distribution of oligomerization states of proteins in the PDB and compare bacterial vs mammalian... there always will be a question though of whether any bias is inherent in proteins or driven by crystallizability itself. Personally, I always though that bacterial

Re: [ccp4bb] High-order oligomers vs robust crystals - references?

Hi, hard evidence I could not find. I once cited "An approach to crystallizing proteins by synthetic symmetrization" for a publication on a rescue strategy in crystallization. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/ They reference to a Phd thesis from 2003. And one idea why it

Re: [ccp4bb] [External] [ccp4bb] High-order oligomers vs robust crystals - references?

Hi Frank, Once we could not crystallize a monomer protein, but we knew the structure of a homolog dimer. We made some educated guessed mutations to dimerize our monomer target, which were based on the structure of the dimeric homolog. Perhaps evidence or perhaps just luck? :-) https://pubmed

Re: [ccp4bb] [External] [ccp4bb] High-order oligomers vs robust crystals - references?

Recently there were few articles where synthetic symmetrization was used to enhance the crystallizability. proteins used were MBP, lysozyme and GFP to name a few. you can search for it. one of them is - https://www.sciencedirect.com/science/article/pii/S0969212615002890 [https://ars.els-cdn.com/

[ccp4bb] High-order oligomers vs robust crystals - references?

Hello all Two decades ago, I remember (!) much talk about a reason that bacterial proteins crystallize "more easily" is that they tend to come as oligomers (dimers and up), and that this internal symmetry made them happier to crystallize. Did anybody ever publish hard evidence?  Or even, is

[ccp4bb] Senior Scientist, Structural Biology position at Sanofi US - Boston area

We are seeking a Scientist to join our Boston-area structural biology group conducting drug design research in diverse therapeutic areas. Our group integrates with multidisciplinary project teams to accelerate drug discovery on innovative and challenging targets using x-ray crystallography and c

Re: [ccp4bb] simulation of structural changes in the protein

Any molecular dynamics simulation would have a temperature parameter. GROMACS is free and easy to use. And do find a computational biology expert to consult with if this is more than an excercise. On Wed, Nov 10, 2021, 11:20 PM Dr Muhammad Saleem wrote: > Dear All, > > I was wondering if there i

Re: [ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

Hi Kyle DynDom gives you the angle of the relative domain movement, which I also find a good quantitative measure. http://dyndom.cmp.uea.ac.uk/dyndom/runDyndom.jsp Best Sabine On 12/11/2021 15:13, Edwin Pozharski wrote: https://pymolwiki.org/index.php/Rms_cur

Re: [ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

https://pymolwiki.org/index.php/Rms_cur On Fri, Nov 12, 2021, 9:05 AM Kyle Gregory < 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear CCP4 bulletin board, > > I was wondering if there are any tools to determine the RMSD of the entire > molecule (two domains) when only aligning one dom

[ccp4bb] Tools for measuring RMSD of entire molecule when a single domain is aligned

Dear CCP4 bulletin board, I was wondering if there are any tools to determine the RMSD of the entire molecule (two domains) when only aligning one domain, the point i'm trying to make is a variation in domain positioning relative to one another but I'd like to quantify it. LSQ alignment in coot

[ccp4bb] Postdoctoral Position Available in Leiden

Hi All! The Armstrong lab is recruiting a postdoctoral fellow with extensive experience in structural biology for a 3 year, funded project to study human and viral enzymes that modify carbohydrates. A PhD in Biochemistry, Biophysics, Structural Biology (or a related field), experience in protei

[ccp4bb] ReNaFoBiS/FRISBI Webinar : Structural Biology Response to Biomedical Threats

Dear All, You are invited to the December ReNaFoBiS/FRISBI Zoom webinar. When: Dec 8, 2021 04:00 PM Paris Webinar Speaker Dr. Wladek Minor (Harrison Distinguished Professor, Department of Molecular Physiology and Biological Physics, University of Virginia, USA) Topic: Structural Biology Re