title: Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions.
abstract: Hydrogen bonding is a key contributor to the molecular recognition between ligands and their host molecules in biological systems. Here we develop a novel orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds observed in 44,585 protein-ligand complexes. We find a close correspondence between the empirical knowledge and the energy landscape inferred from the distribution of HBs. A scoring function based on the resultant hydrogen-bonding potentials discriminates native protein-ligand structures from incorrectly docked decoys with remarkable predictive power.
authors: Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. myzheng@mail.shcnc.ac.cn
authors: Mingyue
authors: M
authors: Zheng
authors: Bing
authors: B
authors: Xiong
authors: Cheng
authors: C
authors: Luo
authors: Shanshan
authors: S
authors: Li
authors: Xian
authors: X
authors: Liu
authors: Qianchen
authors: Q
authors: Shen
authors: Jing
authors: J
authors: Li
authors: Weiliang
authors: W
authors: Zhu
authors: Xiaomin
authors: X
authors: Luo
authors: Hualiang
authors: H
authors: Jiang
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D030562:Databases, Protein; D015195:Drug Design; D006801:Humans; D006860:Hydrogen Bonding; D051188:Knowledge Bases; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012107:Research Design; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins