title: LigBuilder 2: a practical de novo drug design approach.
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.
authors.affiliation: BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.
authors.forename: Yaxia
authors.initials: Y
authors.lastname: Yuan
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Pei
authors.forename: Luhua
authors.initials: L
authors.lastname: Lai
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D015195:Drug Design; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000819:agonists / Q000037:antagonists & inhibitors / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins