RE: May I get your help?

From: Zhijun Li <>
Date: Fri, 11 Jul 2003 10:22:30 -0500

There are some researchers in our center doing the similar protein docking
work. My understanding of Yingliang's question is it at least implies two
questions: (i) How good the output of a rigid docking program? (ii) Will
NMR-derived constraints help improve the output docking complex?

Obviously, like David said, the answers to either one depend on various
factors such as how flexible the protein system, what kind of algorithum is
employed in the docking program, how "bad" the initial structure, etc.

Generally speaking, employing NMR-derived constraints to refine the docking
complex is a good idea. However, obtaining them could be a painful and
time-consuming process. Therefore, it's probably a better idea to carefully
consider all the factors and especially check your docking model against all
the available experimental data before setting out to collect NMR data.

These are just my two cents. Hope it's helpful.


>===== Original Message From "David A. Case" <> =====
>On Wed, Jul 09, 2003, Wu Yingliang wrote:
>> I have a docked protein complex from rigid docking program. It is necessary
>> to build NMR constraints to refine protein complex? I will appreciate very
>> much warm-hearted direction for me as a new user of Amber7.
>I don't really understand the question. Do you have NMR data that you wish
>to interpret, or refine structures into. The answer will probably also
>upon what you mean by "refine the protein complex", i.e. on what you are
>planning to do with the results; it will also depend on how "bad" the initial
>strucutre you have is (i.e. how far away from some "correct" answer it is.)
>.hope this helps...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 |

---------Zhijun Li, Ph.D-------------
-------Dept. of Chemistry&-----------
-------Center for Stru. Bio.-----------
-----_Vanderbilt University-------_----
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Received on Fri Jul 11 2003 - 16:53:01 PDT
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