LigBuilder v2.0 is a multiple-purposed program developed for structure-based de novo drug design and optimization. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them. Main features of LigBuilder v2.0 include:
(1) Cavity: The program detects and analyzes the ligand-binding site of the target protein. CavityScore is calculated as an index to the ligandability of the binding site. A receptor-based pharmacophore model is also suggested by Cavity.
(2) Build: The main module of LigBuilder v2.0. Main functions of Build are, a) Exploring design, b) Lead optimization, c) Fragment linking, d) Mimic design, e) Binding-affinity estimation, f)ligand filtering, g)ligand recommendation, h)Synthesis analysis, i)Substructure Search, j)Molecule clustering.
(3) Fragment Database: Ligand 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.
(4) Forbidden Database: Chemical rules are adopted for evaluating "drug-likeness" of the resultant molecules.
(5) Toxicity Database: Chemical rules are adopted for evaluating toxicity of the resultant molecules.
(6) Synthesis Database: Synthesis feasibility could be taken into account by retro-synthesis procedure.
(7) All the input and output molecules are presented in popular format, i.e. protein in PDB format, ligand in Sybyl Mol2 format and picture in SVG format.
(8) The program is well designed for computer cluster and distributed calculation.
(9) LigBuilder v2.0 is very easy to use. Especially, automatic mode will provide users an one-stop experience in drug design.
(10) LigBuilder v2.0 could provide final report pages for design results with synthesis rountines.
For more detailed description of LigBuilder v2.0, please refer to:
Yaxia Yuan; Jianfeng Pei; Luhua Lai, "LigBuilder 2: A Practical de Novo Drug Design Approach",J. Chem. Inf. Model., 2011, 51 (5), pp 1083–1091
And the reference of LigBuilder v1.2:
Wang, R.; Gao, Y.; Lai, L. "LigBuilder: A Multiple-Purpose Program for Structure-Based Drug Design", J.Mol.Model., 2000, 6, 498-516.
Click here to download the previous version of LigBuilder (version 1.2)
An application of LigBuilder v2.0:
Shuaishuai Ni, Yaxia Yuan, Jin Huang, etc. "Discovering Potent Small Molecule Inhibitors of Cyclophilin A Using de Novo Drug Design Approach", J. Med. Chem. 2009, 52, 5295–5298
LigBuilder v2.0 is written in ANSI C++ and has been tested on UNIX and LINUX platforms. OpenBabel was called directly to convert molecules to SVG format and generating FP2 fingerprint, so an OpenBabel version 2.3.0 or later should be installed first. And, you may need graphical molecular modeling software to prepare the input files and check the resultant molecules.
The LigBuilder v2.0 program is developed by Yaxia Yuan based on the previous version LigBuilder v1.2 developed by Dr. Renxiao Wang. Copyright of the LigBuilder v2.0 program belongs to the Institute of Physical Chemistry, Peking University, China.
[Content] [Introduction] [Download] [Install] [Overview] [CAVITY] [BUILD] [Skills] [FAQs]
(These web pages are edited by Yaxia Yuan. Latest update: Jan, 2012)