Questions about the molecular docking problem

Wen-shyong Tzou wstzou at GATE.SINICA.EDU.TW
Tue Nov 28 10:50:47 EST 1995


Dear Dr. Park:
	There are some references for you where I found in this newsgroup and 
BIOSYM_DEBUG mailing list to consider those questions, though maybe they 
cannot solve all your questions.

	Curr Opin Struct Biol, VOl 3, 265 (1993) and references therein
	J. Comp Chem, Vol 15, 1403 (1994)
	
	BIOSYM_DEBUG : gopher://biox.embnet.unibas.ch:13020/11/ 

I hope it will help.

   ____________________________________________________________________
  |                                                                    |
  |    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                   |
  |____________________________________________________________________|

On 28 Nov 1995, S. Park wrote:

> Hello,
> 
> I have been studying the rigid molecular docking problem and have several
> questions about the assumptions typically made.  Since my major is computer
> science, I lack lots of basic knowledge on the subject and I wonder if 
> anyone could kindly tell me about your opinion and give me any references
> that I could use for the study.  I would really appreciate it !
> 
> Here are my questions:
> 
> It seems to me that there are three assumptions for the molecular docking 
> problem:
> 
> 1. Rigidity
> 2. Availability of the atomic coordinates
> 3. Solvent effects related assumption
> 
> First of all, I would like to know how "accurate" the results we have with
> the assumptions above.  For example, I understand that the answers are
> "approximate" solutions for the real answer.  But how reliable (or,
> exact, valid ?) are they ?  Can we quantify this ?
> 
> Secondly, it seems to me that most of the automated docking procedures
> make use of the atomic coordinates of the molecules.  But what if we don't
> have their crystal structures ?  How could we find the mode of binding in
> these cases ?
> 
> Thirdly, I wonder how much information could we glean from the geometric
> complementarity based approach.  I understand that this is a sort of
> "screening" process for later "energy minimization".  It seems to me that
> geometric complementarity serves as a necessary condition for the real
> answer.  But what if we miss the real "answer" in this "screening" step ?
> 
> Finally, I wonder how reliable the result that comes from without considering
> the surrounding solvent is.  It seems to me that one of the reasons that we
> don't consider the solvent effect is due to the expensive computational cost.
> But then how "accurate" is the result ?
> 
> Thank you very much for your time !
> 
> Regards,
> Seongbin Park (separk at pollux.usc.edu)
> 
> 
> 



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