Re: [ccp4bb] Multiple binding model in BLI

binding). I can certainly try KINTEK but am currently not familiar with that software. Thanks. M Chandra On Wed, Aug 28, 2024 at 10:23 AM wrote: > Dear Chandra, > > What exactly do you mean by 1:3 or 1:2 binding mode? Is that > stoichiometry? Do you need/want to fit a simple binding mod

[ccp4bb] Multiple binding model in BLI

which particular equation I need to use to fit the BLI curve into a 1:3 binding model. Any help or suggestion from the community in this matter would be highly appreciated. Thank you, M Chandra To unsubscribe from the

Re: [ccp4bb] CCP4BB vs COVID19

hi There are developments in cyclic and constrained peptides see for example J Am Chem Soc. 2019 Mar 13;141(10):4167-4181. hope it helps On 22/3/2020 8:01 pm, Abhishek Anan wrote: Dear all, Not directly related to the discussion but does any

[ccp4bb] Bidentate GLU vs two monodentate GLU in metalloproteins

Dear all, What is more preferable or conserved by evolution of lifeform point of view between glutamate acting as bidentate ligand by its carboxylate group or two monodentate GLU at metal binding site in natural metalloenzymes. I was thinking 2 GLU are better than one bidentate GLU because if one G

[ccp4bb] Bidentate GLU vs two monodentate GLU in metalloproteins

Dear all, What is more preferable or conserved by evolution point of view between glutamate acting as bidentate ligand by its carboxylate group or two monodentate GLU at metal binding site in natural metalloprotein. I was thinking 2 GLU are better than one bidentate GLU because if one GLU gets muta

[ccp4bb] help

Hello all Does anyone knows of a review that highlights the first examples of the use of NMR combined with X-ray crystallography to solve the structures of proteins thanks chandra

Re: [ccp4bb] Modelling protein/protein interfaces

haddock may be an appropriate tool https://haddock.science.uu.nl/ On 26/1/2018 8:34 PM, Thomas Krey wrote: Dear colleagues, Is there any appropriate tool for docking an interacting protein to a relatively large protein-protein interface (>2500 A2). We are facing a hetero-oligomer for whic

Re: [ccp4bb] Predict effects of mutations on protein stability and protein-protein interaction

duet is quite good too http://biosig.unimelb.edu.au/duet/ On 25/11/2017 1:20 AM, Vivoli, Mirella wrote: Dear Wenhe, I have used iMutant 2.0. I hope it helps. Below the link of a paper related to the prediction server: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160136/ Best, Mirella Get O

[ccp4bb] AutoSol invalid MTZ column_types error

Dear all, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to run AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks a lot in advance. Best, Mi

[ccp4bb] relative domain motion calculation...

Dear All, I am working with a protein containing tandem domains, connected with 3-4 residue linker. I want to calculate the relative motion/orientation of one domain with respect to the hinge region as well as with respect to the other domain. Both the domains have very less seq. identity (<20%). P

[ccp4bb] secondary structure problem...

Dear All, I am refining one of the structure at 3.1 A resolution with R factor and R free of 30 and 34 with setmet peak data. Some of the region in the model look like loops without any secondary structure (helix and strands). Can anybody help me out ??? Mintu.

[ccp4bb] protocol for seleno-methionine incorporation...

should use the purified protein or digested protein for mass spectrometry. Thanks, Mintu Chandra. -- Mintu Chandra Senior Research Fellow IISER BHOPAL mi...@iiserb.ac.in +918085288853

[ccp4bb] Align linux version

Dear CCP4 users, We are trying to align two different structures. It would be helpful for us if anybody has linux compiled align version? Regards, Mintu Chandra

Re: [ccp4bb] off topic: rmsf in simulation

to complement the very nice description by jeremy, you may wish to try and decompose the vibrational modes to get this sense by focussing on the origins of the "red shift" in the vibrational spectrum and this accounts largely for the increased vibrational entropies upon complexation. This

Re: [ccp4bb] Protein-Protein Interactions

evidence to cross check results obtained from other method. Hope it helps Manish Manish Chandra Pathak, Ph.D. Indian Institute of Science Education and Research ITI (Gas Rahat) Building Govindpura, Bhopal 462023 India tel: +91-750-4092340 -- On Thu, Aug 2, 2012 1:28

Re: [ccp4bb] modeling thioester bond

sed between two >different chains. > > >Thanks for the tip, >ciao, >s > > > >On Jul 26, 2012, at 2:19 PM, Manish Chandra Pathak wrote: > > >> >>Just defining LINK in your pdb file should work. Try this format. >>LINK NZ  LYS A 233   

Re: [ccp4bb] sequence format conversion

Guess, you are looking for ReadSeq; with GenBank|gb set as output format. http://www.ebi.ac.uk/cgi-bin/readseq.cgi However, no idea how to get only 10 residues in a line, if you are specific. best Manish > > From: K Singh >To: CCP4BB@JISCMAIL.AC.UK >

Re: [ccp4bb] Self-rotation Patterson maps

Hello John, In my struggle with self-rotation function, I found this extremely useful to start with. Specially the fig 4 on page 107. "Characterizing a Crystal From an Initial Native Dataset" by Michael R. Sawaya http://www.springerlink.com/content/k024q83484477j42/ The peaks in the log fil

[ccp4bb] Post Doc Opportunity to post, please

I would like to have the following Post Doc Research Fellow opportunity posted please. Thanks very much, Chandra *Chandra Farnsworth* *Staffing Consultant* Genentech, Inc. Research and Early Development 650-225-7110

Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

Hi Bashir, In Pymol: 1. Show---Surface (will generate surface around the protein) 2. Setting-Surface---Cavities & Pockets Only. (will show only Cavities inside) 3. Use cavity_cull command to set the filter for cavities. (eg. set cavity_cull, 40) Manish -- Manish Chandra Pa

Re: [ccp4bb] sequence from pdb

Hi Rex, I like this simple and quick server to extract pdb seq. http://swift.cmbi.ru.nl/servers/html/soupir.html Manish -- Manish Chandra Pathak, Ph.D. Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 USA Tel: +1-404-727-2563

Re: [ccp4bb] How to compare the binding affinity between two domains structurally?

if the link between the domains is not part of the interface then perhaps a good first approximation may be to "cut" the linker and then use a program such as APBS to compute the binding energy.. > Hi, > > Recently we determined two structures of the same protein in complex with > different molec

Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

Hi Peter, I think, instead of tightening the weighing term, giving it slight freedom would have helped. If data quality is good at 1.8 ang, then it certainly deserves more freedom. What do you think. best wishes Manish Manish Chandra Pathak, Ph.D. Department of Biochemistry Emory

[ccp4bb] question

well interacting through the same interface but with very different surfaces. the more diverse the interfacial conformations, the better. thanks chandra

Re: [ccp4bb] Regarding BMCD

It is due to your local computer's or LAN's firewall denying access to the port 8060. Is it correct? all the best Manish From: Nishant Varshney To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, June 12, 2009 3:08:14 AM Subject: [ccp4bb] Regarding BMCD Dear all, I

Re: [ccp4bb] PDB protein strucutrues as screen saver

For mac, a screen saver (structure) is already available. moreover it's free and displays couple of structural information exactly the way Jayashankar wants. http://www.sourcecod.com/structure/ I hope their is something like this for Linux/Windows also. F

Re: [ccp4bb] Ligand binding in multiple conformation

An extension of this topic: does anyone know of examples where for complexes between the two proteins A and B, protein A has two different conformations at its interface? thanks chandra -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Aaron

Re: [ccp4bb] Ligand binding in multiple conformation

hi yes this may happen in some circumstanceshave a look at J Am Chem Soc. 2008 Oct 15;130(41):13514-5. > Hi, > > I had a question about flexibility in ligand binding in an enzyme active > site. Is it possible for a substrate/product analogue to bind in more > than > one conformation in the

Re: [ccp4bb] Setting drops with proteins that are hard to concentrate

Dear Matt, In one of our project, the protein of interest used to elute from Ni-column with ~20 other proteins. I also guessed it due to surface Cysteines. Addition of 2mM free Cys in the protein sample helped, which competed with free Cys on the protein surface and, ultimately, gave happy

Re: [ccp4bb] refinement problem of labelled RNA complex

Hi, It's much easier to begin with the cif file created by Refmac5 itself, but this cif file needs to be checked and corrected manually for the restrains. Certainly, Iodine is not happy with the current restrains. Most of the time, i have found problems beginning with the protonation and th

Re: [ccp4bb] .cif file

Hello Vineet, This seems old one and doesn't have all restraints. you may use refmac dictionary for spermine. I am sure this will work in coot also. you may find it at /ccp4-6.0.2/lib/data/monomers/s/SPM.cif thanks Manish Vineet Gaur <[EMAIL PROTECTED]> wrote: Hi all I am using COOT for