A practical Java tool for small-molecule compound appraisal

Amani, Parisa, Sneyd, Todd, Preston, Sarah, Young, Neil D., Mason, Lyndel, Bailey, Ulla-Maja, Baell, Jonathan, Camp, David, Gasser, Robin B, Gorse, Alain-Dominique, Taylor, Paul and Hofmann, Andreas (2015) A practical Java tool for small-molecule compound appraisal. Journal of Cheminformatics, 7 1: 28.1-28.4. doi:10.1186/s13321-015-0079-1

Author Amani, Parisa
Sneyd, Todd
Preston, Sarah
Young, Neil D.
Mason, Lyndel
Bailey, Ulla-Maja
Baell, Jonathan
Camp, David
Gasser, Robin B
Gorse, Alain-Dominique
Taylor, Paul
Hofmann, Andreas
Title A practical Java tool for small-molecule compound appraisal
Journal name Journal of Cheminformatics   Check publisher's open access policy
ISSN 1758-2946
Publication date 2015-06-16
Sub-type Article (original research)
DOI 10.1186/s13321-015-0079-1
Open Access Status DOI
Volume 7
Issue 1
Start page 28.1
End page 28.4
Total pages 4
Place of publication London, United Kingdom
Publisher Chemistry Central
Language eng
Formatted abstract
Background: 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.
Keyword Compound appraisal
Molecular properties
Personal database
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2016 Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 5 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 5 times in Scopus Article | Citations
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