chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery
Abstract Background Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of command line programs with a wide range of functionaliti...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13321-017-0228-9 |
| _version_ | 1818579787715706880 |
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| author | Man-Ling Lee Ignacio Aliagas Jianwen A. Feng Thomas Gabriel T. J. O’Donnell Benjamin D. Sellers Bernd Wiswedel Alberto Gobbi |
| author_facet | Man-Ling Lee Ignacio Aliagas Jianwen A. Feng Thomas Gabriel T. J. O’Donnell Benjamin D. Sellers Bernd Wiswedel Alberto Gobbi |
| author_sort | Man-Ling Lee |
| collection | DOAJ |
| description | Abstract Background Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of command line programs with a wide range of functionalities for cheminformatics. The chemalot_knime package allows command line programs that read and write SD files from stdin and to stdout to be wrapped into KNIME nodes. The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster. Results Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure–activity or property analysis and other type of investigations, (2) The creation of a quantitative structure–property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database. Conclusions The chemalot and chemalot_knime packages provide lightweight and powerful tools for many tasks in cheminformatics. They are easily integrated with other open source and commercial command line tools and can be combined to build new and even more powerful tools. The chemalot_knime package facilitates the generation and maintenance of user-defined command line workflows, taking advantage of the graphical design capabilities in KNIME. Graphical abstract Example KNIME workflow with chemalot nodes and the corresponding command line pipe |
| first_indexed | 2024-12-16T07:07:15Z |
| format | Article |
| id | doaj.art-edfb9c52e3044076802ecdada87add4f |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-16T07:07:15Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-edfb9c52e3044076802ecdada87add4f2022-12-21T22:40:00ZengBMCJournal of Cheminformatics1758-29462017-06-019111410.1186/s13321-017-0228-9chemalot and chemalot_knime: Command line programs as workflow tools for drug discoveryMan-Ling Lee0Ignacio Aliagas1Jianwen A. Feng2Thomas Gabriel3T. J. O’Donnell4Benjamin D. Sellers5Bernd Wiswedel6Alberto Gobbi7Discovery Chemistry, Genentech Inc.Discovery Chemistry, Genentech Inc.Denali TherapeuticsKNIME.com AGgNova Scientific SoftwareDiscovery Chemistry, Genentech Inc.KNIME.com AGDiscovery Chemistry, Genentech Inc.Abstract Background Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of command line programs with a wide range of functionalities for cheminformatics. The chemalot_knime package allows command line programs that read and write SD files from stdin and to stdout to be wrapped into KNIME nodes. The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster. Results Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure–activity or property analysis and other type of investigations, (2) The creation of a quantitative structure–property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database. Conclusions The chemalot and chemalot_knime packages provide lightweight and powerful tools for many tasks in cheminformatics. They are easily integrated with other open source and commercial command line tools and can be combined to build new and even more powerful tools. The chemalot_knime package facilitates the generation and maintenance of user-defined command line workflows, taking advantage of the graphical design capabilities in KNIME. Graphical abstract Example KNIME workflow with chemalot nodes and the corresponding command line pipehttp://link.springer.com/article/10.1186/s13321-017-0228-9Command line programSubstructure identificationProperty calculationSARQSPR modelConformation analysis |
| spellingShingle | Man-Ling Lee Ignacio Aliagas Jianwen A. Feng Thomas Gabriel T. J. O’Donnell Benjamin D. Sellers Bernd Wiswedel Alberto Gobbi chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery Journal of Cheminformatics Command line program Substructure identification Property calculation SAR QSPR model Conformation analysis |
| title | chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery |
| title_full | chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery |
| title_fullStr | chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery |
| title_full_unstemmed | chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery |
| title_short | chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery |
| title_sort | chemalot and chemalot knime command line programs as workflow tools for drug discovery |
| topic | Command line program Substructure identification Property calculation SAR QSPR model Conformation analysis |
| url | http://link.springer.com/article/10.1186/s13321-017-0228-9 |
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