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Bioinformatics. 2017 Jun 1;33(11):1747-1749. doi: 10.1093/bioinformatics/btx037.

Ligandbook: an online repository for small and drug-like molecule force field parameters.

Author information

1
Department of Biochemistry, University of Oxford, Oxford, UK.
2
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
3
Department of Physics, Arizona State University, Tempe, AZ, USA.
4
Center for Biological Physics, Arizona State University, Tempe, AZ, USA.
5
Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, Gif-sur-Yvette, France.

Abstract

Summary:

Ligandbook 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 Implementation:

Ligandbook 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.

Contact:

oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org .

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28130228
PMCID:
PMC5447236
DOI:
10.1093/bioinformatics/btx037
[Indexed for MEDLINE]
Free PMC Article

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