ADL: Energy Minimization

Lenin Dominguez 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
webpage: http://www.paginasprodigy.com/wtigger/Site/Welcome.html

"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." 
Cornish-Bowden, 1995

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> 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:
> 
> http://www.ddl.unimi.it/vega/index.htm
> 
> 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:
> 
> www.expasy.ch/spdbv/
> 
> Then you also have NAMD and GROMACS, which are more robust when it
> comes to energy minimization.
> 
> Cheers,
> Michel
> 
> 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/
>>  prodrg.html)
>>
>>  Does anyone happen to know of any other programmes accepting PDB
>>  structures for energy minimisation?
>>
>>  Thanks
>>
>>  George
>>
>>
>>  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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>>
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