Docking

Wen-shyong Tzou wstzou at GATE.SINICA.EDU.TW
Thu Nov 16 11:07:56 EST 1995


Dear Sir:
	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 ).
	My questions are :
(1) Is there any automatic way to do that ? ( BCL ? )
(2) It has been known that minimization will reduce large amounts of van 
der Waals repulsive energy. Is the interaction energy term after 
minimization trustable to be served as the criteria of patterns of 
interaction of two proteins ? Where can I find a better way ?

Any suggestion will be appreciated and summarized.

	Wen-shyong Tzou 
   ____________________________________________________________________
  |                                                                    |
  |    Wen-shyong Tzou                 Email:wstzou at gate.sinica.edu.tw |
  |    Graduate student                                                |
  |    Computer Simulation Laboratory        http://www.sinica.edu.tw/ |
  |    Institute of Biomedical Science       Phone:(886)-2-789-9033    |
  |    Academia Sinica                       Fax:  (886)-2-782-5573    |
  |    Taipei, Taiwan, R.O.C.                                          |
  |                                                                    |
  |    Address:P.O.Box 1-99, Nankang, Taipei, Taiwan                   |
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