Open Babel: An open chemical toolbox

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dc.contributor.author O'Boyle, Noel M.
dc.contributor.author Banck, Michael
dc.contributor.author James, Craig A.
dc.contributor.author Morley, Chris
dc.contributor.author Vandermeersch, Tim
dc.contributor.author Hutchison, Geoffrey R.
dc.date.accessioned 2011-11-29T13:28:18Z
dc.date.available 2011-11-29T13:28:18Z
dc.date.copyright 2011
dc.date.issued 2011-10-07
dc.identifier.citation O'Boyle, NM; Banck, M; James, CA; Morley, C; Vandermeersch, T; Hutchison, GR (2011) 'Open Babel: An open chemical toolbox'. Journal of cheminformatics, 3:33. en
dc.identifier.volume 3 en
dc.identifier.startpage 33 en
dc.identifier.issn 1758-2946
dc.identifier.uri http://hdl.handle.net/10468/466
dc.identifier.doi 10.1186/1758-2946-3-33
dc.description.abstract Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. en
dc.description.sponsorship Health Research Board (PD/2009/13) en
dc.description.uri http://openbabel.org en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Chemistry Central en
dc.relation.uri http://www.jcheminf.com/content/3/1/33
dc.rights © 2011 O'Boyle et al; licensee Chemistry Central Ltd. en
dc.rights.uri http://creativecommons.org/licenses/by/2.0/ en
dc.subject Chemical structures en
dc.subject Chemical informatics en
dc.subject Open Babel en
dc.subject.lcsh Molecular structure en
dc.title Open Babel: An open chemical toolbox en
dc.type Article (peer-reviewed) en
dc.internal.authorurl http://publish.ucc.ie/researchprofiles/C019/noboyle en
dc.internal.authorcontactother Noel O'Boyle, School Of Pharmacy, University College Cork, Cork, Ireland. +353-21-490-3000 Email: n.oboyle@ucc.ie en
dc.internal.availability Full text available en
dc.date.updated 2011-11-25T08:50:50Z
dc.description.version Published Version en
dc.internal.rssid 114582669
dc.contributor.funder Health Research Board en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Journal of cheminformatics en
dc.internal.copyrightchecked Yes The license is CC-BY 2.0. Checked Sherpa RoMEO. en
dc.internal.licenseacceptance Yes en
dc.internal.IRISemailaddress n.oboyle@ucc.ie en


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© 2011 O'Boyle et al; licensee Chemistry Central Ltd. Except where otherwise noted, this item's license is described as © 2011 O'Boyle et al; licensee Chemistry Central Ltd.
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