title: COPICAT: a software system for predicting interactions between proteins and chemical compounds.
abstract: Since tens of millions of chemical compounds have been accumulated in public chemical databases, fast comprehensive computational methods to predict interactions between chemical compounds and proteins are needed for virtual screening of lead compounds. Previously, we proposed a novel method for predicting protein-chemical interactions using two-layer Support Vector Machine classifiers that require only readily available biochemical data, i.e. amino acid sequences of proteins and structure formulas of chemical compounds. In this article, the method has been implemented as the COPICAT web service, with an easy-to-use front-end interface. Users can simply submit a protein-chemical interaction prediction job using a pre-trained classifier, or can even train their own classification model by uploading training data. COPICAT's fast and accurate computational prediction has enhanced lead compound discovery against a database of tens of millions of chemical compounds, implying that the search space for drug discovery is extended by >1000 times compared with currently well-used high-throughput screening methodologies.
  
  
  BACKGROUND
  The COPICAT server is available at http://copicat.dna.bio.keio.ac.jp. All functions, including the prediction function are freely available via anonymous login without registration. Registered users, however, can use the system more intensively.
authors.affiliation: Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan. yasu@bio.keio.ac.jp
authors.forename: Yasubumi
authors.initials: Y
authors.lastname: Sakakibara
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Hachiya
authors.forename: Miho
authors.initials: M
authors.lastname: Uchida
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Nagamine
authors.forename: Yohei
authors.initials: Y
authors.lastname: Sugawara
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yokota
authors.forename: Masaomi
authors.initials: M
authors.lastname: Nakamura
authors.forename: Kris
authors.initials: K
authors.lastname: Popendorf
authors.forename: Takashi
authors.initials: T
authors.lastname: Komori
authors.forename: Kengo
authors.initials: K
authors.lastname: Sato
mesh_terms: D016208:Databases, Factual; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D060388:Support Vector Machine
chemical_list: D008024:Ligands; D011506:Proteins