ADL: Energy Minimization
acheron24 at hotmail.com
Thu Mar 6 14:58:14 PST 2008
UCSF Chimera is great with protein PDBs and extremely easy to use.
Dr. Lenin Domínguez-Ramírez
Departamento de Bioquímica
Facultad de Medicina
Universidad Nacional Autonoma de Mexico
Avenida Universidad 3000
Circuito Escolar, Ciudad Universitaria
México 04510 D.F., MEXICO
Tel: (5255) 56232259
e-mail: jdoming at ifc.unam.mx
"And for all the current and rather silly emphasis on structural
biology,understanding enzymes means understanding catalysis and
catalysis is concerned with kinetics, not structure: as Jeremy
Knowles aptly remarked, studying the photograph of a racehorse cannot
tell you how fast it can run."
> Date: Thu, 6 Mar 2008 13:20:59 -0600
> From: mef at ddt.biochem.umn.edu
> To: autodock at scripps.edu
> Subject: Re: ADL: Energy Minimization
> Yes. For small molecules you can use VEGA:
> This is a free program that can perform energy minimization at
> semiempirical level. Pretty good and easy to use.
> For proteins, the easiest program to use is the Swiss PDB viewer:
> Then you also have NAMD and GROMACS, which are more robust when it
> comes to energy minimization.
> On Thu, Mar 6, 2008 at 1:07 PM, George Tzotzos wrote:
>> The Dundee PRODRG2 Server has the functionality of energy
>> minimisation (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
>> Does anyone happen to know of any other programmes accepting PDB
>> structures for energy minimisation?
>> On Mar 6, 2008, at 6:11 PM, Mihaly Mezei wrote:
>> >> Is energy minimization necessary since autodock is just going to
>> >> twist the molecule around anyway? It seems like an unnecessary
>> >> step to me, and it looks like that is what you just quoted in from
>> >> the J. Comp. Chem. article.
>> > Actually, it is important to energy minimize, since the binding
>> > free energy estimate includes the energy of the ligand in the
>> > initial conformation. I once found a ligand whose binding free
>> > energy was estimated as ca -50 kcal/mol, due to some clashes int he
>> > initial conformation.
>> > Mihaly Mezei
>> > Department of Structural and Chemical Biology, Mount Sinai School
>> > of Medicine, NYU
>> > Voice: (212) 659-5475 Fax: (212) 849-2456
>> > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/
>> > profile.do?id=0000072500001497192632
>> > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
>> > ________________________________________________
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