title: Spresso: an ultrafast compound pre-screening method based on compound decomposition.
abstract: BACKGROUND
  Recently, the number of available protein tertiary structures and compounds has increased. However, structure-based virtual screening is computationally expensive owing to docking simulations. Thus, methods that filter out obviously unnecessary compounds prior to computationally expensive docking simulations have been proposed. However, the calculation speed of these methods is not fast enough to evaluate ≥ 10 million compounds.
  
  
  RESULTS
  In this article, we propose a novel, docking-based pre-screening protocol named Spresso (Speedy PRE-Screening method with Segmented cOmpounds). Partial structures (fragments) are common among many compounds; therefore, the number of fragment variations needed for evaluation is smaller than that of compounds. Our method increases calculation speeds by ∼200-fold compared to conventional methods.
  
  
  METHODS
  Spresso is written in C ++ and Python, and is available as an open-source code (http://www.bi.cs.titech.ac.jp/spresso/) under the GPLv3 license.
  
  
  BACKGROUND
  akiyama@c.titech.ac.jp.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, School of Computing, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Yanagisawa
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.|Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Shunta
authors.initials: S
authors.lastname: Komine
authors.affiliation: Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.|Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Shogo D
authors.initials: SD
authors.lastname: Suzuki
authors.affiliation: Department of Computer Science, School of Computing, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.
authors.forename: Masahito
authors.initials: M
authors.lastname: Ohue
authors.affiliation: Department of Computer Science, School of Computing, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.|Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Ishida
authors.affiliation: Department of Computer Science, School of Computing, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.|Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.|Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama
mesh_terms: D062105:Molecular Docking Simulation / Q000379:methods*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure; D012984:Software
chemical_list: D011506:Proteins