Molecular modeling annual

, Volume 6, Issue 7, pp 498–516

LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design

Authors

  • Renxiao Wang
    • Institute of Physical ChemistryPeking University
  • Ying Gao
    • Institute of Physical ChemistryPeking University
    • Institute of Physical ChemistryPeking University
Original Article

DOI: 10.1007/s0089400060498

Cite this article as:
Wang, R., Gao, Y. & Lai, L. J Mol Model (2000) 6: 498. doi:10.1007/s0089400060498

Abstract

We have developed a new multi-purpose program, LigBuilder, for structure-based drug design. Within the structural constraints of the target protein, LigBuilder builds up ligands step by step using a library of organic fragments. Various operations, such as growing, linking, and mutation, have been implemented to manipulate molecular structures. The user can choose either growing or linking strategies for ligand construction and a genetic algorithm is adopted to control the whole construction process. Binding affinities of the ligands are estimated by an empirical scoring function and the bioavailabilities are evaluated by a set of chemical rules. Using thrombin and dihydrofolate reductase as examples, we have demonstrated that LigBuilder is able to generate chemical structures similar to the known ligands.

Keywords

Structure-based drug designAutomatic ligand constructionFragment-based approachGenetic algorithm
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Copyright information

© Springer-Verlag Berlin Heidelberg 2000