Abstract
BackgroundThe 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.ResultsThe 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.ConclusionscApp 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0079-1) contains supplementary material, which is available to authorized users.
Highlights
The increased use of small-molecule compound screening by new users from a variety of different aca‐ demic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments
Screening of organic small-molecule compounds has been a pivotal activity in the pharmaceutical industry as part of the drug discovery process
Access to the PubChem Compound Database is through the PubChem Power User Gate (PUG), which is an XML-based communication gateway to interrogate the database
Summary
Software features cApp is a personal compound database software that allows the user to compare chemical descriptors and similarities of compounds, and to annotate compound lists with their own data and information. In the compound appraisal task, cApp conducts SMARTS queries using 480 PAINs substructure filters that have been translated from the original rules in Sybyl Line Notation (sln) by Dr Rajarshi Guha We compared the results of PAINs-filtering in cApp with those obtained by the original sln rules The results from this benchmarking indicate that there are small variations in the queries conducted by different software (see Table 1)
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