title: CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering.
abstract: Similarity-based clustering and classification of compounds enable the search of drug leads and the structural and chemogenomic studies for facilitating chemical, biomedical, agricultural, material and other industrial applications. A database that organizes compounds into similarity-based as well as scaffold-based and property-based families is useful for facilitating these tasks. CFam Chemical Family database http://bidd2.cse.nus.edu.sg/cfam was developed to hierarchically cluster drugs, bioactive molecules, human metabolites, natural products, patented agents and other molecules into functional families, superfamilies and classes of structurally similar compounds based on the literature-reported high, intermediate and remote similarity measures. The compounds were represented by molecular fingerprint and molecular similarity was measured by Tanimoto coefficient. The functional seeds of CFam families were from hierarchically clustered drugs, bioactive molecules, human metabolites, natural products, patented agents, respectively, which were used to characterize families and cluster compounds into families, superfamilies and classes. CFam currently contains 11,643 classes, 34,880 superfamilies and 87,136 families of 490,279 compounds (1691 approved drugs, 1228 clinical trial drugs, 12,386 investigative drugs, 262,881 highly active molecules, 15,055 human metabolites, 80,255 ZINC-processed natural products and 116,783 patented agents). Efforts will be made to further expand CFam database and add more functional categories and families based on other types of molecular representations.
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China Computational and Systems Biology, Singapore-MIT Alliance, National University of Singapore, Singapore.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456 yzchen@cz3.nus.edu.sg.
authors.forename: Lin
authors.initials: L
authors.lastname: Tao
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456.
authors.forename: Chu
authors.initials: C
authors.lastname: Qin
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543.
authors.forename: Shangying
authors.initials: S
authors.lastname: Chen
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543.
authors.forename: Xian
authors.initials: X
authors.lastname: Zeng
authors.affiliation: College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China State Key Laboratory of Medicinal Chemistry & Biology, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin 300457, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Medicinal Chemistry & Biology, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin 300457, China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
authors.forename: Sheng Yong
authors.initials: SY
authors.lastname: Yang
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China yzchen@cz3.nus.edu.sg.
authors.forename: Yu Zong
authors.initials: YZ
authors.lastname: Chen
mesh_terms: D001688:Biological Products / Q000145:classification; D016000:Cluster Analysis; D062126:Databases, Chemical; D055808:Drug Discovery; D006801:Humans; D020407:Internet; D004364:Pharmaceutical Preparations / Q000145:classification
chemical_list: D001688:Biological Products; D004364:Pharmaceutical Preparations