Dataset Information
Spresso: an ultrafast compound pre-screening method based on compound decomposition.
Ontology highlight
ABSTRACT: Motivation
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.Availability and implementation
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.Contact
akiyama@c.titech.ac.jp.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Yanagisawa K
PROVIDER: S-EPMC5860314 | biostudies-literature | 2017 Dec
REPOSITORIES: biostudies-literature
Publications
Spresso: an ultrafast compound pre-screening method based on compound decomposition.
Bioinformatics (Oxford, England) 20171201 23
<h4>Motivation</h4>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.<h4>Results</h4>In this article, we propose a nov ...[more]
