Subject: Summary: flexible docking program

From: Renxiao Wang <[email-masked]>
Date: Mon, 24 Jan 2000 12:00:02 -0800 (PST)

Hi, everybody!

Two weeks ago we posted a message looking for a docking program that can
handle the flexibility of the receptor. It seems that the answers focus on
InsightII/affinity and Sybyl/FlexX. Here are the details:

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Date: Mon, 24 Jan 2000 09:55:33 +0100 
From: [email-masked] (Pieter Stouten) 

You might want to look at Affinity from MSI (URL
http://www.msi.com/life/products/insight/modules/affinity.html).  It is an
automatic docking module for Insight II that incorporates Monte Carlo and
simulated annealing methods to place a ligand within a receptor.  The
method is designed so that after the Monte Carlo phase the receptor within
the defined binding site is flexible by default.  In other words, all you
have to do is define the extent of the binding site.  Every receptor atom
within that region is flexible and free to move. 

Recent publications using Affinity are: 

1.  Kurinov, I. V., Myers, D. E., Irvin, J. D., Uckun, F. M. 1999. X-ray
crystallographic analysis of the structural basis for the interactions of
pokeweed antiviral protein with its active site inhibitor and ribosomal
RNA substrate analogs. Prot. Sci. 8:1765-72

2.  Read, M. A., Wood, A. A., Harrison, J. R., Gowan, S. M., Kelland, L. 
R., et al. 1999. Molecular Modeling Studies on G-Quadruplex Complexes of
Telomerase Inhibitors: Structure-Activity Relationships. J. Med. Chem. San
Diego, CA 92121

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Date: Mon, 17 Jan 2000 19:15:29 -0800 
From: Andre de Oliveira <[email-masked]>

Try FlexX available in Sybyl (www.tripos.com).

(This procedure allows the user to define rotatable torsions both on
ligand and receptor. It uses a genetic algorithm to sample conformations
and uses force field to estimate the interaction energy.) 

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Date: Tue, 18 Jan 2000 10:12:21 -0500 
From: Shaomeng Wang <[email-masked]>

(Prof. Wang's group has developed a new method to perform flexible
docking. But I am not sure whether the program is available now.)

You may want to check out the following publications from my group. 

Pak, Y. and Wang, S. Application of a new molecular dynamics simulation
method with a generalized effective potential to the flexible docking
problems. J. Physical Chemistry,(B), 2000, 104, 354-359. 

Pak, Y. and Wang, S. Folding of a 16-residue helical peptide using
molecular dynamics simulation with Tsallis effective potential, J.
Chemical Physics, 1999, 111, 4359-4361.

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All my best wishes,

Arthur

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| Dr. Renxiao Wang                                                     | 
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| Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104  | 
| University of California Los Angeles     | Los Angeles, CA90066      | 
| Los Angeles, CA 90024                    | U.S.A                     | 
| Phone: 310-8250269 (Lab)                 | Phone: 310-3904638 (Home) | 
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| E-mail: [email-masked]                                        | 
| WWW: http://zimbu.chem.ucla.edu/~arthur/                             |
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