[ccp4bb] rigid flexible analysis

Hi everyone! I would like to know the current online servers available for analyzing the rigid and flexible regions of proteins.Looking forward for precious inputs from the community. Sincerely, Dr. Gauri Misra Assistant Professor Amity Institute of Biotechnology Amity University Noida (U.P

Re: [ccp4bb] determination of oligomerization state of protein

Hi, Try glutaraldehyde crosslinking of peaks you are obtaining from SEC individually and see if it gives you some idea. Best wishes Gauri

Re: [ccp4bb] Protein thermostability

adapted to perform under stress conditions. Gauri Misra et al. Proteins: Structure, Function, and Bioinformatics Volume 76, Issue 2, <http://onlinelibrary.wiley.com/doi/10.1002/prot.v76:2/issuetoc> pages 496–506, 1 August 2009 Hope it gives you some help. Best wishes, Gauri On Sat, Jun 30, 2

[ccp4bb] off topic question

Hi, A nuclear receptor is purified only in the presence of strong affinity bound ligand. Is there some method to study and quantitate binding affinities of this protein with other ligands (it is bound to the high affinity ligand after purification)? Attempts to purify in presence of low affinity li

Re: [ccp4bb] mutation and minimization

You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder > Hi Andreas, > > > I would like to introduce point mutations in a structure and quickly >> (and dirtily) minimize the new residue. (Best rotamer dependent on local >> environment, or the like.) What are simple approaches that don't involve

[ccp4bb] GST tag digestion conditions

Hi everyone, This is although an off topic question but I would certainly seek expert advices on the following query: I have a GST-tagged protein that is purified in presence of the steroids. I carry out an in column digestion using thrombin. Digestion buffer compositin: 50mM Tris pH: 8.0, 150m

Re: [ccp4bb] Methods to calculate the importance of mutated residue on the stability of protein

Hi Keat, Check this http://cupsat.tu-bs.de/ (CUPSAT: Cologne University Protein Stability Analysis Tool) Hope it serves your purpose. Gauri On Wed, Apr 13, 2011 at 9:50 AM, Heng Keat Tam < t...@bio.chemie.uni-freiburg.de> wrote: > Dear all, > > Do anyone know the way to estimate the importance

Re: [ccp4bb] how to quantitate protein which dont have ne aromatic residue

Hi, You can read the spectrophotometric absorption at 280 nm and 200nm in UV range. It should serve your purpose and provide a decent idea for the amount of protein in the sample. Provided that absorbance at 280nm is given by aromatic rings but at the same time absorbance at 200nm is contributed by

[ccp4bb] Question about GST cleavage

Just an offshoot of the same Question.. I would like to ask whether the same applies for GST-tag digestion using thrombin.. No agitation gives better results in the above case too... Any personal experiences On Thu, Mar 31, 2011 at 11:29 AM, Klaus Piontek < klaus.pion...@ocbc.uni-freiburg.de>

Re: [ccp4bb] kinase purification

You can use ATP agarose for purification and include the cofactor required right from expression till purification steps. On Tue, Mar 29, 2011 at 8:10 PM, Neeraj Kapoor wrote: > Hi All, > I am trying to express a kinase but unfortunately there is aggregation > happening as the protein is pur

Re: [ccp4bb] protein aggregation

.de> wrote: > > 2 M urea and detergents > > On Wed, 23 Mar 2011 13:41:55 -0400 > gauri misra wrote: > > Hi, > > What are the different methods to prevent protein aggregation while > > concentrating so as to increase the concentration of the protein? > >

[ccp4bb] protein aggregation

Hi, What are the different methods to prevent protein aggregation while concentrating so as to increase the concentration of the protein? I have some idea of adding EDTA and charged amino acids like L-Arg and L-Glu. I would appreciate if the readers share their experiences. Thanks! Gauri

Re: [ccp4bb] Can procheck or other tools report bad geometry for ligand?

Hi, Swiss-pdb viewer works well for small peptides, you can check if it serves your objective too... Even WHAT IF provides clues to bond angles, bond length and torsion angles. Gauri On Thu, Mar 10, 2011 at 3:56 PM, Robert Immormino wrote: > Hi Halliang, > If the ligands are in the pdb het dicti

Re: [ccp4bb] determining the domain for overexpression and crystallization

Hi, To start with it would be great if you look in to the secondary structure prediction of the sequence using any of the standard servers like PSIPRED, JPRED etc. Many more available at expasy site http://ca.expasy.org/tools/. Whatever construct you finally choose to make just remember the standar

Re: [ccp4bb] Looking for the following values...

Hi, Generally if we use CCP4i we can find these details easily in scala log files. Gauri On Thu, Jan 13, 2011 at 2:48 PM, J. Fleming wrote: > Hi All, > > I'm about ready to deposit my structure and have used pdb_extract to aid > in the process. Unfortunately the following values were not fou

Re: [ccp4bb] creat a model with insertion

Hi Chen, Check SPDBViewer if it is of some help to you! Gauri On Thu, Jan 13, 2011 at 5:57 AM, Qing Chen wrote: > Dear all, > > I have the wt protein structure that contains two domains. I want to creat > a model with two glycerin inserted between the two domains. > Which software or webserver c

Re: [ccp4bb] superpositioning two ligands

Dear Rex, You can try SPDB viewer if it serves your purpose. Gauri

Re: [ccp4bb] dissolving peptides !

Rashmi, You can try 1%DMSO and also acetonitrile but the former is preferable. Gauri On Mon, Jun 7, 2010 at 3:04 AM, rashmi panigrahi < rashmi.panigrah...@gmail.com> wrote: > Hello everybody, > I have a 16 mer peptide which is predicted to be positively charged alpha > helix and has 50% of its s

Re: [ccp4bb] Alignment software

Try ESPript.. Gauri

[ccp4bb] refines Query for non covalent interactions

Thanks to all for responding.. Infact precisely i am looking for some server that can calculate hydrogen bonds, electrostatic interactions, and hydrophobic interactions present in various pdbs...simultaneously Cheers GM

[ccp4bb] noncovalent interactions

Hi, Which free online servers are best for calculation of non covalent interactions present in several pdb structures? Thanks for any insights provided by the community members... Cheers GM

[ccp4bb] 2,3-butanediol

Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri