Abstract
SummaryLigandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes.Availability and ImplementationLigandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
The computational drug design process relies on the parameterization of atomic interactions through empirical force fields in order to probe protein–drug interactions with classical molecular dynamics or Monte Carlo simulations
A reference repository for small molecule parameters generated by other means and especially for ones published in the literature is lacking
The repository contains more than 2900 packages, formatted for use with GROMACS (Abraham et al, 2015). These include 455 parameter sets that were validated with hydration free energy calculations as part of the SAMPL challenges (Beckstein and Iorga, 2012; Beckstein et al, 2014; Kenney et al, 2016), parameters from some of our previous studies (Simmons et al, 2014), and > 2000 packages with ligands from the PDB, parameterized with MOL2FF
Summary
The computational drug design process relies on the parameterization of atomic interactions through empirical force fields in order to probe protein–drug interactions with classical molecular dynamics or Monte Carlo simulations. A reference repository for small molecule parameters generated by other means and especially for ones published in the literature is lacking. Such published parameters are valuable because they have typically been validated and can be used in new studies but they can be difficult to find and are often invisible to most searches, e.g. as part of supplementary information. Very specialized repositories for force field parameters exist: The Gromacs molecule & liquid database (Fischer et al, 2015; van der Spoel et al, 2012) contains about 500 parameter sets Ligandbook aims to enable parameter re-use and simulation reproducibility by (i) facilitating the publication of force field parameters as open data; (ii) acting as an archive for parameter sets that are supplied and maintained by the community; (iii) making large, richly annotated parameter datasets available through human and machine accessible interfaces
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
