Subject: Release of LigBuilder beta version

From: Arthur Wang <[email-masked]>
Date: Thu, 29 Apr 1999 09:39:27 -0700 (PDT)

Dear CCLers,

    We would like to announce that the beta version of LigBuilder is now
available to the public. 

    LigBuilder is a general-purposed program package written for structure
-based drug design procedure. Based on the 3D structure of the target
protein, it can automatically build ligand molecules within the binding
pocket. Manuscripts describing LigBuilder in details are currently under
preparation. In brief, main features of LigBuilder are: 

(1) When the program analyzes the binding pocket of the target protein, it
    derives the pharmacophore model as a by-product. Such a model could be
    applied to 3D database searching.

(2) User can choose to develop derivatives on a "core" structure (growing
    strategy) or link several separated groups into an integrated molecule
    (linking strategy).

(3) Molecules are built up by using fragmental building blocks. Various
    kinds of structure manipulation are provided, such as growing, linking,
    and mutation. The fragment library is user maintainable.

(4) On-the-fly minization of conformation is performed while building the
    molecules. All the conformations corresponding to energy minima are
    accepted.

(5) Molecules are evolved iteratively by applying Genetic Algorithm. The
    fitness score of a molecule is evaluated both by its binding affinity
    with the target protein and its chemical viability.

(6) Lipinski rules are applied to screen out molecules which are not "drug-
    like". Molecules containing any "forbidden" substructure are also
    rejected. The "forbidden" substructure library is user maintainable.

(7) All the input and output molecules are in popular format, i.e. protein
    in PDB format and ligands in Sybyl Mol2 format.

    The program is written in C++ and run on UNIX/LINUX workstation.

    We sincerely invite you to test this program. You can download the
program via anonymous FTP to ftp.ipc.pku.edu.cn/pub/software/LigBuilder/.
Any feedback will be highly appreciated. And we will make necessary 
modification on LigBuilder based on your suggestion. 

    With best wishes,

    Arthur

    _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
    _/   Renxiao Wang                     Doctoral Candidate      _/
    _/   Molecular Design Laboratory                              _/
    _/   Institute of Physical Chemistry, Peking University       _/
    _/   Beijing 100871, P.R.China                                _/
    _/                                                            _/ 
    _/   E-mail: [email-masked]                            _/
    _/   Tel: 86-10-62751490    Fax: 86-10-62751725               _/
    _/   WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html       _/
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