BioRetroSynth2017-09-29T12:44:10+00:00/groups/13192018-07-26T13:02:53+00:00Pablo Carbonell shared KNIME Workflow for RetroRules and SelenzymeKNIME Workflow for RetroRules and Selenzyme This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool. 1. Input to the workflow: Chemical reactions expressed using public database identifiers. 2. Each reaction queries RetroRules and outputs the corresponding reaction rules. 3. Each reaction rule queries Selenzyem and outputs the selected Uniprot sequences for each rule. 4. Resulting list of selected enzymes is stored in a csv file for further processing. Release: r20180811 How to cite Duigou T, Du Lac, M., Carbonell P, Faulon JL. RetroRules: a database of reaction rules for engineering biology. Please report bugs to pablo.carbonell@manchester.ac.uk Worfklow Licence: CC BY-SA P. Carbonell & T. …urn:uuid:ce97e7ae-e8e4-4861-983b-a062e4c5b083Pablo Carbonell2018-07-26T13:02:03+00:00Pablo Carbonell shared KNIME Workflow for RetroRules and Retropath2.0KNIME Workflow for RetroRules and RetroPath2.0 This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers. 1. Input to the workflow: Chemical reactions expressed using public database identifiers. 2. Each reaction queries RetroRules and outputs the corresponding reaction rules. 3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format. Installation notes The workflow runs a Python scrpt that requires pandas: Python Data Analysis Library. In order to setup the Python Extension, please check the KNIME documentation:  https://www.knime.com/blog/how-to-setup-the-python-extension Release: r20180811   How to cite Duigou T, Du Lac, M., Carbonell P, Faulon JL. RetroRules: a database of reaction rules for enginee …urn:uuid:0d75e4cd-f677-48b0-8157-fbd2f9bd2239Pablo Carbonell2017-10-12T13:23:02+00:00Thomas Duigou shared RetroPath2.0-Mods-isomer-transformation-queueThe workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. It is a modified version of "RetroPath2.0-Mods-isomer-transformation". It illustrates how to introduce a FIFO data structure for the source set and use it for iteratively firing rules on small chunks of structures. See [1] for details.   How to use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.4.1 of Knime Analytics Platform. Licence: CC BY-NC-SA This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ . Koch M, Duigou T, Carbonell P & Faulon JL, 12/10/2017   [ …urn:uuid:6f334676-3003-4095-b15f-eeb37d9e76f0Thomas Duigou2017-09-29T12:44:10+00:00Baudoin Delépine joined the BioRetroSynth groupurn:uuid:6b97723b-9f6d-4535-967a-38762eec202dBaudoin Delépine2017-06-30T17:15:13+00:00Thomas Duigou shared RetroPath2.0-Mods-metabolomicsSet of workflows for the "Metabolome completion and metabolomics" use case: 1) Produces a list of molecules using a user defined set of rules (RetroPath2.0 workflow). 2) Takes as input the products generated by RetroPath2.0 and prepare the files to be read by OpenMS nodes. 3) The last workflow finally searches for each produced compound the corresponding peak in some MS spectra. See [1] for details.   How to use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. Licence: CC BY-NC-SA This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ . Koch M, …urn:uuid:19d5620c-095f-4a15-94af-9ffcc4081e56Thomas Duigou2017-06-30T17:09:48+00:00Thomas Duigou shared Aminoglycosides-DataData to be used with the RetroPath2.0-Mods-iQSAR and QSAR-model-aminoglycosides workflows for the "search for molecules maximizing biological activities" use case: - Source and Rules input. - Pre-generated Results. - Training set for building the QSAR of the antibacterial activity.urn:uuid:93ef0ca2-4707-4321-9bae-8f65a76410b2Thomas Duigou2017-06-30T17:05:59+00:00Thomas Duigou shared QSAR-model-aminoglycosidesThe workflow build a QSAR model with LOO cross-validation for antibacterial activities of aminoglycosides structures using RDKit fingerprints and random forest. See [1] for details. Antibacterial activities were compiled from Setny et al, JCIM, 2009.   How to use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. Licence: CC BY-NC-SA This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ . Koch M, Duigou T, Carbonell P & Faulon JL, 22/06/2017   [1] Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screenin …urn:uuid:a8d51b20-f12b-49ec-9e5e-ef37f14162c6Thomas Duigou2017-06-30T17:03:35+00:00Thomas Duigou shared RetroPath2.0-Mods-iQSARThe workflow allows one to search chemical structures in the chemical space optimizing biological activites. See [1] for details.   How to use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. Licence: CC BY-NC-SA This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ . Koch M, Duigou T, Carbonell P & Faulon JL, 22/06/2017   [1] Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-025 …urn:uuid:d28954b3-84f1-4181-a884-fb172ad70d5bThomas Duigou2017-06-30T17:01:25+00:00Thomas Duigou shared Monomers-DataData to be used with the RetroPath2.0-Mods-isomer-augmentation and QSAR-model-Tg-prediction workflows for the monomer enumeration use case: - Source and Rules input. - Pre-generated Results. - Training set for building the QSAR of the glass transition temperature.urn:uuid:9c866d9e-f61c-4d93-b598-79fe4d15be25Thomas Duigou2017-06-30T16:57:42+00:00Thomas Duigou shared Alkane-Enumeration-DataData to be used with the RetroPath2.0-Mods-isomer-transformation workflow for the alkane enumeration use case: - Source and Rules input. - Pre-generated Results.urn:uuid:e29673a4-ba82-44c9-8feb-ffe5883630e0Thomas Duigou2017-06-30T16:55:10+00:00Thomas Duigou shared QSAR-model-Tg-predictionThe workflow (i) build a QSAR model for Tg prediction with LOO cross-validation and (ii) predict the Tg for enumerated isomers. See [1] for details. Tg values were compiled from Brown et al, JCIM, 2006.   How to use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. Licence: CC BY-NC-SA This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ . Koch M, Duigou T, Carbonell P & Faulon JL, 22/06/2017   [1] Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journ …urn:uuid:9ce3a8c8-c92d-4ed1-b63f-ce93fdc53ec4Thomas Duigou2017-06-30T16:52:39+00:00Thomas Duigou shared RetroPath2.0-Mods-isomer-transformationThe workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. See [1] for details.   How to use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. Licence: CC BY-NC-SA This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ . Koch M, Duigou T, Carbonell P & Faulon JL, 22/06/2017   [1] Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017 …urn:uuid:9e6446c7-2811-455e-bd58-4de2a415232aThomas Duigou