Subject: Free CADD software release: LigBuilder v1.0

From: Gao Ying <[email-masked]>
Date: Wed, 15 Sep 1999 10:55:41 -0700 (PDT)

Dear CCLers,

  We announce here that LigBuilder v1.0 is now available. You can download
it free via anonymous FTP to ftp2.ipc.pku.edu.cn/pub/software/LigBuilder. 

  LigBuilder is a multiple-purposed program written for structure-based
drug design procedure. Based on the three-dimensional structure of the
target protein, it can automatically build ligand molecules within the
binding pocket and subsequently screen them. 

  In brief, main features of LigBuilder include: 

  (1) The program analyzes the binding pocket of the target protein and
derives the key interaction sites. A pharmacophore model is suggested and
it could be applied to 3D database searching. 

  (2) User can choose to develop ligand molecules by growing strategy or
linking strategy. Either lead discovery or lead optimization tasks can be
carried out. 

  (3) Molecules are built up by using fragment as building blocks. 
Various kinds of structure manipulation are provided, such as growing,
linking, and mutation. On-the-fly minimization of conformation is
performed during the building-up procedure. The flexibility of the ligand
molecules is considered. 

  (4) Molecules are evolved by Genetic Algorithm. The fitness score of a
molecule is evaluated by considering its chemical viability as well as
binding affinity. 

  (5) Chemical rules for judging "drug-likeness" are applied to screen the
resultant molecules. Chemical stability, synthesis feasibility, and
toxicity can also be taken into account by defining "forbidden structure" 
libraries. 

  (6) All the input and output molecules are in popular format, i.e. 
protein in PDB format and ligand in Sybyl Mol2 format. The program is very
easy to use and maintain. 

  LigBuilder is written in C++ language and has been tested on UNIX,
LINUX, and DOS platforms. 

  If you encounter any problem while downloading the program, please
contact Ms. Ying Gao at [email-masked]. 

  Please forward this mail to anyone who may concern. 

  With best wishes,

  Molecular Design Laboratory, Institute of Physical Chemistry
  Peking University, Beijing, China