Original Article

Molecular modeling annual

, Volume 6, Issue 7, pp 498-516

First online:

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

  • Renxiao WangAffiliated withInstitute of Physical Chemistry, Peking University
  • , Ying GaoAffiliated withInstitute of Physical Chemistry, Peking University
  • , Luhua LaiAffiliated withInstitute of Physical Chemistry, Peking University Email author 

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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.


Structure-based drug design Automatic ligand construction Fragment-based approach Genetic algorithm