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Re: [ccp4bb] Fwd: [ccp4bb] site mutation evaluation |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Fwd: site mutation evaluation From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU Date: 2008-12-03 And this is what I call just in time publication: Davis et al. RosettaLigand Docking with Full Ligand and Receptor Flexibility. J Mol Biol (2008) pp. available online today. Jürgen On 3 Dec 2008, at 01:47, David Briggs wrote: > Hi there > > Assuming you have a model of the complex you are interested in > tinkering with, try submitting it to the Rosetta Alanine Scanning > servery thing. > http://robetta.bakerlab.org/alascansubmit.jsp > > By default, it mutates each residue in the interface to ala, does some > local minimisation (side chains only, I seem to recall) and then re > calculates the binding energy. You can also give it lists of other > mutants to try. > > If your data is sensitive , you can download the rosetta software and > do it yourself - the rosetta software is a little complicated > sometimes though. > > HTH, > > David. > > 2008/12/3 junfeng liu >> Hi Hongmin, >> That should need some docking softwares or the structures of the >> complex. >> ta >> liu >> Hongmin Zhang wrote: >>> >>> Thanks! I think we still can't tell if the mutant would disturb >>> ligand >>> binding or not. >>> Best! >>> Hongmin >>> >>> On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch >>> >>> >>> In that case you might want to use CNS with model_anneal.inp or >>> model_minimize.inp, or the equivalents in phenix >>> >>> Jürgen >>> >>> On 2 Dec 2008, at 21:29, Hongmin Zhang wrote: >>> >>>> Yes, it is better to have MD or energy minimization. Otherwise, >>>> with only view on the screen, we can't tell if the mutated >>>> residue would disturb ligand binding because of the side chain >>>> flexibility. >>>> Best! >>>> Hongmin >>>> >>>> On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch >>>> >>>> >>>> Pymol >>>> the question is, into how much trouble do you want to get ? >>>> MD simulations ? Energy minimisation ? Then you will need to >>>> do more than just mutate on the sreen one residue with Pymol. >>>> >>>> Jürgen >>>> >>>> On 2 Dec 2008, at 17:29, Hongmin Zhang wrote: >>>> >>>> Dear All, >>>> I am trying to mutate a single amino acid in a PDB to >>>> see if the mutant >>>> disturbs ligand binding. Does anyone know any software >>>> that can do such work? >>>> Thanks a lot! >>>> >>>> >>>> - >>>> Jürgen Bosch >>>> University of Washington >>>> Dept. of Biochemistry, K-426 >>>> 1705 NE Pacific Street >>>> Seattle, WA 98195 >>>> Box 357742 >>>> Phone: +1-206-616-4510 >>>> FAX: +1-206-685-7002 >>>> Web: http://faculty.washington.edu/jbosch >>>> >>>> The information in this e-mail is intended only for the >>>> person to whom it is >>>> addressed. If you believe this e-mail was sent to you in >>>> error and the e-mail >>>> contains patient information, please contact the Partners >>>> Compliance HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was >>>> sent to you in error >>>> but does not contain patient information, please contact the >>>> sender and properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> - >>> Jürgen Bosch >>> University of Washington >>> Dept. of Biochemistry, K-426 >>> 1705 NE Pacific Street >>> Seattle, WA 98195 >>> Box 357742 >>> Phone: +1-206-616-4510 >>> FAX: +1-206-685-7002 >>> Web: http://faculty.washington.edu/jbosch >>> >>> >> > > > > -- > ============================ > David C. Briggs PhD > Father & Crystallographer > http://drdavidcbriggs.googlepages.com/home > AIM ID: dbassophile > ============================ - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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