title: A practical Java tool for small-molecule compound appraisal.
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.
authors.affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia.
authors.forename: Parisa
authors.initials: P
authors.lastname: Amani
authors.affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia.
authors.forename: Todd
authors.initials: T
authors.lastname: Sneyd
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC Australia.
authors.forename: Sarah
authors.initials: S
authors.lastname: Preston
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC Australia.
authors.forename: Neil D
authors.initials: ND
authors.lastname: Young
authors.affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia.
authors.forename: Lyndel
authors.initials: L
authors.lastname: Mason
authors.affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia.
authors.forename: Ulla-Maja
authors.initials: UM
authors.lastname: Bailey
authors.affiliation: Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences (MIPS), Monash University, Parkville, VIC Australia.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Baell
authors.affiliation: Griffith School of Environment, Griffith University, Nathan, QLD Australia.
authors.forename: David
authors.initials: D
authors.lastname: Camp
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC Australia.
authors.forename: Robin B
authors.initials: RB
authors.lastname: Gasser
authors.affiliation: Queensland Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD Australia.
authors.forename: Alain-Dominique
authors.initials: AD
authors.lastname: Gorse
authors.affiliation: School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Taylor
authors.affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia ; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC Australia.
authors.forename: Andreas
authors.identifier: 0000-0003-4408-5467
authors.initials: A
authors.lastname: Hofmann
keywords: Compound appraisal; Molecular properties; Personal database