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Re: [ccp4bb] site mutation evaluation |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: site mutation evaluation From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK Date: 2008-12-03 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 > > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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