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Updated: Jun 2, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
LigBuilder 2: a practical de novo drug design approach
Yaxia Yuan1, Jianfeng Pei, Luhua Lai
1BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.
Abstract:
We have developed a new version (2.0) of the de novo drug design program LigBuilder. With LigBuilder 2.0, the synthesis accessibility of designed compounds can be analyzed, and a cavity detection procedure is implemented to detect the positions and shapes of the binding sites on the surface of a given protein structure and to quantitatively estimate drugability. Ligands are designed to best fit the detected cavities using a set of rules for evaluation. Drug-like and privileged fragments are used to construct the ligands with the aid of internal and external absorption, distribution, metabolism, excretion, and toxicity (ADME/T) and drug-like filters.
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