Re: information

From: David A. Case <>
Date: Sun, 1 Jun 2003 17:14:29 -0700

On Thu, May 29, 2003, aram joel panay wrote:

> I?m interested in calculations of binding energy for protein-protein,
> protein-peptide; a colleague told me the AMBER program might be useful...

> how can I get the software package?

See the amber web page:

> how big are the proteins this program can manage?
> What type of hardware I need to run the program?
> And something very important, how friendly this program is? Because we work
> in molecular biology, but not in physical chemistry, so no one has strong
> skills in the management of this kind of software.

Calculating binding energies for proteins + peptides (and especially for
proteins + proteins) is a very challenging task. It appears that any reliable
calculation of protein/protein association energies is not yet possible, even
for the most experienced users. In any event, you should expect to invest
a significant effort, in learning computers, in learning about simulation
techniques, and in interpreting the data and their probable errors, if you
expect to get any interesting results.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Mon Jun 02 2003 - 01:53:01 PDT
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