title: LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.
abstract: LISE is a web server for a novel method for predicting small molecule binding sites on proteins. It differs from a number of servers currently available for such predictions in two aspects. First, rather than relying on knowledge of similar protein structures, identification of surface cavities or estimation of binding energy, LISE computes a score by counting geometric motifs extracted from sub-structures of interaction networks connecting protein and ligand atoms. These network motifs take into account spatial and physicochemical properties of ligand-interacting protein surface atoms. Second, LISE has now been more thoroughly tested, as, in addition to the evaluation we previously reported using two commonly used small benchmark test sets and targets of two community-based experiments on ligand-binding site predictions, we now report an evaluation using a large non-redundant data set containing >2000 protein-ligand complexes. This unprecedented test, the largest ever reported to our knowledge, demonstrates LISE's overall accuracy and robustness. Furthermore, we have identified some hard to predict protein classes and provided an estimate of the performance that can be expected from a state-of-the-art binding site prediction server, such as LISE, on a proteome scale. The server is freely available at http://lise.ibms.sinica.edu.tw.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Zhong-Ru
authors.initials: ZR
authors.lastname: Xie
authors.forename: Chuan-Kun
authors.initials: CK
authors.lastname: Liu
authors.forename: Fang-Chih
authors.initials: FC
authors.lastname: Hsiao
authors.forename: Adam
authors.initials: A
authors.lastname: Yao
authors.forename: Ming-Jing
authors.initials: MJ
authors.lastname: Hwang
mesh_terms: D001665:Binding Sites; D020407:Internet; D008024:Ligands; D010770:Phosphotransferases / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins; D010770:Phosphotransferases