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 <[EMAIL PROTECTED]>: > 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 <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> wrote: >> >> 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 >>> <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: >>> >>> 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 ============================
