A practical Java tool for small-molecule compound appraisal

Parisa Amani, Todd Sneyd, Sarah Preston, Neil David Young, Lyndel Mason, Ulla-Maja Bailey, Jonathan Bayldon Baell, David G Camp, Robin Beat Gasser, Alain-Dominique Gorse, Paul R Taylor, Andreas Hofmann

Research output: Contribution to journalArticleResearchpeer-review

Abstract

The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments. While software and spreadsheet solutions exist, there is a need for software that can be easily deployed and is convenient to use. Results: The Java application cApp addresses this need and aids in the handling and storage of information on small-molecule compounds. The software is intended for the appraisal of compounds with respect to their physico-chemical properties, analysis in relation to adherence to likeness rules as well as recognition of pan-assay interference components and cross-linking with identical entries in the PubChem Compound Database. Results are displayed in a tabular form in a graphical interface, but can also be written in an HTML or PDF format. The output of data in ASCII format allows for further processing of data using other suitable programs. Other features include similarity searches against user-provided compound libraries and the PubChem Compound Database, as well as compound clustering based on a MaxMin algorithm. Conclusions: cApp is a personal database solution for small-molecule compounds which can handle all major chemical formats. Being a standalone software, it has no other dependency than the Java virtual machine and is thus conveniently deployed. It streamlines the analysis of molecules with respect to physico-chemical properties and drug discovery criteria; cApp is distributed under the GNU Affero General Public License version 3 and available from http://www.structuralchemistry.org/pcsb/. To download cApp, users will be asked for their name, institution and email address. A detailed manual can also be downloaded from this site, and online tutorials are available at http://www.structuralchemistry.org/pcsb/capp.php.
Original languageEnglish
Article number28
Number of pages4
JournalJournal of Cheminformatics
Volume7
Issue number1
DOIs
Publication statusPublished - 2015

Cite this

Amani, P., Sneyd, T., Preston, S., Young, N. D., Mason, L., Bailey, U-M., ... Hofmann, A. (2015). A practical Java tool for small-molecule compound appraisal. Journal of Cheminformatics, 7(1), [28]. https://doi.org/10.1186/s13321-015-0079-1
Amani, Parisa ; Sneyd, Todd ; Preston, Sarah ; Young, Neil David ; Mason, Lyndel ; Bailey, Ulla-Maja ; Baell, Jonathan Bayldon ; Camp, David G ; Gasser, Robin Beat ; Gorse, Alain-Dominique ; Taylor, Paul R ; Hofmann, Andreas. / A practical Java tool for small-molecule compound appraisal. In: Journal of Cheminformatics. 2015 ; Vol. 7, No. 1.
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abstract = "The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments. While software and spreadsheet solutions exist, there is a need for software that can be easily deployed and is convenient to use. Results: The Java application cApp addresses this need and aids in the handling and storage of information on small-molecule compounds. The software is intended for the appraisal of compounds with respect to their physico-chemical properties, analysis in relation to adherence to likeness rules as well as recognition of pan-assay interference components and cross-linking with identical entries in the PubChem Compound Database. Results are displayed in a tabular form in a graphical interface, but can also be written in an HTML or PDF format. The output of data in ASCII format allows for further processing of data using other suitable programs. Other features include similarity searches against user-provided compound libraries and the PubChem Compound Database, as well as compound clustering based on a MaxMin algorithm. Conclusions: cApp is a personal database solution for small-molecule compounds which can handle all major chemical formats. Being a standalone software, it has no other dependency than the Java virtual machine and is thus conveniently deployed. It streamlines the analysis of molecules with respect to physico-chemical properties and drug discovery criteria; cApp is distributed under the GNU Affero General Public License version 3 and available from http://www.structuralchemistry.org/pcsb/. To download cApp, users will be asked for their name, institution and email address. A detailed manual can also be downloaded from this site, and online tutorials are available at http://www.structuralchemistry.org/pcsb/capp.php.",
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Amani, P, Sneyd, T, Preston, S, Young, ND, Mason, L, Bailey, U-M, Baell, JB, Camp, DG, Gasser, RB, Gorse, A-D, Taylor, PR & Hofmann, A 2015, 'A practical Java tool for small-molecule compound appraisal' Journal of Cheminformatics, vol. 7, no. 1, 28. https://doi.org/10.1186/s13321-015-0079-1

A practical Java tool for small-molecule compound appraisal. / Amani, Parisa; Sneyd, Todd; Preston, Sarah; Young, Neil David; Mason, Lyndel; Bailey, Ulla-Maja; Baell, Jonathan Bayldon; Camp, David G; Gasser, Robin Beat; Gorse, Alain-Dominique; Taylor, Paul R; Hofmann, Andreas.

In: Journal of Cheminformatics, Vol. 7, No. 1, 28, 2015.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Baell, Jonathan Bayldon

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Amani P, Sneyd T, Preston S, Young ND, Mason L, Bailey U-M et al. A practical Java tool for small-molecule compound appraisal. Journal of Cheminformatics. 2015;7(1). 28. https://doi.org/10.1186/s13321-015-0079-1