ANNOUNCE: LigBuilder v1.2

[Gao Ying <gao (- at -) linux2.ipc.pku.edu.cn>]

 Dear All,
   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 search for finding novel
 ligand molecules.
     (2) Molecules are constructed by using fragments as building blocks.
 Various kinds of structural manipulation are provided, such as
 growing, linking, and mutation. On-the-fly minimization of conformation is
 performed during the building-up procedure. While the
 target protein is kept rigid, flexibility of the ligand molecules is
 considered.
     (3) User can choose either growing strategy or linking strategy to
 develop ligand molecules.
     (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 are adopted for evaluating "drug-likeness" of
 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 presented in popular
 format, i.e. protein in PDB format and ligand in Sybyl Mol2 format. The
 program is very easy to use.
    LigBuilder is written in ANSI C++ and has been tested on UNIX and LINUX
 platforms. Running LigBuilder itself does not need any other software.
 However, you may need a graphical molecular modeling software to prepare
 the input files and check the resultant molecules.
   If you encounter any problem while downloading the program, please
 contact Ms. Ying Gao at gao (- at -) mdl.ipc.pku.edu.cn.
   If you are the old user of LigBuilder and have not received the encrypt
 key, please contact Ms. Ying Gao at gao (- at -) mdl.ipc.pku.edu.cn.
   Please forward this mail to anyone who may concern.
   With best wishes,
   Molecular Design Laboratory, Institute of Physical Chemistry
   Peking University, Beijing, China