Docking

Henry Gabb gabb at europa.lif.icnet.uk
Fri Nov 17 05:06:54 EST 1995


Wen-shyong Tzou (wstzou at GATE.SINICA.EDU.TW) wrote:

: 	I have two proteins which are supposed to interact with each
: other. I want to figure out whch way they interact . My strategy now ( 
: based on the biochemical data ) is to align these two proteins along 
: their axis, rotate or translate one of them ( certainly, not exhaustively ), 
: and then calculate their interaction energy ( after zero minimization ).

: (1) Is there any automatic way to do that ? ( BCL ? )

There are several automated methods to do what you're asking.  Most of
them are summarized in the following reference:

Cherfils and Janin, Curr Opin Struct Biol, 3, 265 (1993).

As far as minimizing two docked proteins, the following reference
contains an algorithm to do it without disrupting the structures too
much:

Gibson and Scheraga, J Comp Chem, 15, 1403 (1994).

The program described in this reference is available from QCPE
(reference number 659).

Good luck.

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|  Henry Gabb                                 (gabb at icrf.icnet.uk)   |
|  Imperial Cancer Research Fund                                     |
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|  London WC2A 3PX                                                   |
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