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A practical Java tool for small-molecule compound appraisal.

Amani P, Sneyd T, Preston S, Young ND, Mason L, Bailey UM, Baell J, Camp D, Gasser RB, Gorse AD, Taylor P, Hofmann A - J Cheminform (2015)

Bottom Line: 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. 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.

View Article: PubMed Central - PubMed

Affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia.

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.

No MeSH data available.


Related in: MedlinePlus

Screenshot of a project in the graphical user interface of cApp. Different tasks (appraisal, similarity searches) or sets of one project appear under different tabs. Views of a particular compound in the Jmol molecular viewer and the JChemPaint chemical editor are available with a single mouse-click. The project shown illustrates an appraisal task (loaded from the file ‘test.smi’). Views of CMPD288 in the Jmol molecular viewer as well as the JChemPaint chemical editor are activated.
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Fig1: Screenshot of a project in the graphical user interface of cApp. Different tasks (appraisal, similarity searches) or sets of one project appear under different tabs. Views of a particular compound in the Jmol molecular viewer and the JChemPaint chemical editor are available with a single mouse-click. The project shown illustrates an appraisal task (loaded from the file ‘test.smi’). Views of CMPD288 in the Jmol molecular viewer as well as the JChemPaint chemical editor are activated.

Mentions: cApp is a personal compound database software that allows the user to compare chemical descriptors and similarities of compounds, but also to annotate compound lists with their own data and information. A cApp project comprises all data and compound sets of a software session; a compound set is a particular list of compounds. In the GUI, a compound set is displayed as a table on a particular tab (see Figure 1). Automatically generated HTML, PDF and ASCII presentations of compound sets are identified by their set number. Conceptually, its functionality is divided up into tasks, presentation of results and convenience features. In the present version, the tasks of compound appraisal, similarity search and clustering can be performed. The compound appraisal task calculates physico-chemical properties and structural features, an analysis for compliance with various likeness criteria (drug-, lead- or fragment-like) [16] and the identification of PAINs components [17] using the SMSD maximum common subgraph (MCS) Tanimoto coefficient as criterion [18]. Similarity searches against user-provided libraries can be conducted using an MCS approach which builds on the CDK Fingerprint Tanimoto coefficient [18] or the PubChem Compound Database. For compound clustering, a MaxMin algorithm with subsequent k-Means clustering [19] has been implemented, based on the CDK Fingerprint Tanimoto coefficient as property. The user can annotate compounds with extra information by adding three types of data in additional columns containing either free text, a file link or a URL. Linked files and web content are available with a mouse click from the cApp GUI via the user’s preferred web browser.Figure 1


A practical Java tool for small-molecule compound appraisal.

Amani P, Sneyd T, Preston S, Young ND, Mason L, Bailey UM, Baell J, Camp D, Gasser RB, Gorse AD, Taylor P, Hofmann A - J Cheminform (2015)

Screenshot of a project in the graphical user interface of cApp. Different tasks (appraisal, similarity searches) or sets of one project appear under different tabs. Views of a particular compound in the Jmol molecular viewer and the JChemPaint chemical editor are available with a single mouse-click. The project shown illustrates an appraisal task (loaded from the file ‘test.smi’). Views of CMPD288 in the Jmol molecular viewer as well as the JChemPaint chemical editor are activated.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4469258&req=5

Fig1: Screenshot of a project in the graphical user interface of cApp. Different tasks (appraisal, similarity searches) or sets of one project appear under different tabs. Views of a particular compound in the Jmol molecular viewer and the JChemPaint chemical editor are available with a single mouse-click. The project shown illustrates an appraisal task (loaded from the file ‘test.smi’). Views of CMPD288 in the Jmol molecular viewer as well as the JChemPaint chemical editor are activated.
Mentions: cApp is a personal compound database software that allows the user to compare chemical descriptors and similarities of compounds, but also to annotate compound lists with their own data and information. A cApp project comprises all data and compound sets of a software session; a compound set is a particular list of compounds. In the GUI, a compound set is displayed as a table on a particular tab (see Figure 1). Automatically generated HTML, PDF and ASCII presentations of compound sets are identified by their set number. Conceptually, its functionality is divided up into tasks, presentation of results and convenience features. In the present version, the tasks of compound appraisal, similarity search and clustering can be performed. The compound appraisal task calculates physico-chemical properties and structural features, an analysis for compliance with various likeness criteria (drug-, lead- or fragment-like) [16] and the identification of PAINs components [17] using the SMSD maximum common subgraph (MCS) Tanimoto coefficient as criterion [18]. Similarity searches against user-provided libraries can be conducted using an MCS approach which builds on the CDK Fingerprint Tanimoto coefficient [18] or the PubChem Compound Database. For compound clustering, a MaxMin algorithm with subsequent k-Means clustering [19] has been implemented, based on the CDK Fingerprint Tanimoto coefficient as property. The user can annotate compounds with extra information by adding three types of data in additional columns containing either free text, a file link or a URL. Linked files and web content are available with a mouse click from the cApp GUI via the user’s preferred web browser.Figure 1

Bottom Line: 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. 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.

View Article: PubMed Central - PubMed

Affiliation: Structural Chemistry Program, Eskitis Institute, Griffith University, Nathan, QLD Australia.

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.

No MeSH data available.


Related in: MedlinePlus