Docking Two Molecules

Jacqueline Duquesne duquesne at alioth.inria.fr
Thu Apr 28 08:08:39 EST 1994

I am studying the Docking problem:
Given two rigid molecules (the ligand and the receptor), each of them modeled by a set of Van der Waals
spheres, predict the structure and binding free energy of a ligand-receptor

We have developped an algorithm to predict some possible structures of a ligand-receptor
complex, and now we need to filter out the best one(s).

I would appreciate your advice on the two following subjects:

1) What are the classical examples of ligand-receptor complex which are used to test docking algorithms ?

You may either tell me the names of the molecules (I have ftp access to the
Protein Data Bank (PDB)) or send me some files of 3D structures (at least x,y,z
coordinates for each atom).  

If you want some results on some specific molecules you are working on, I will also
be pleased to try my algorithm on these. 

2) Let's say that I have a set of predicted structures for a ligand-receptor
complex. What do you think would be the best criterion to keep only the best ones ?

- In Theory ?

- On a practical basis:
For example, do you have a numerical formula to compute the free energy ?

As you will notice, I don't know as much as you about chemistry, because my field
is Computational Geometry and I work on algorithms for spheres. I am very
interested in applications in chemistry, and I would like some simple answers,
i.e. with not too much chemical details. Don't worry, I may ask for the details later !

Thank you for your answers. I will post a summary.

Jacqueline Duquesne		E-mail: duquesne at sophia.inria.fr
Project PRISME			Tel: (33) 93 65 77 49
INRIA Sophia Antipolis		Fax: (33) 93 65 76 43
2004, route des Lucioles	B.P. 93
06902 Sophia Antipolis Cedex	France

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