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 |
|____________________________________________________________________|
