JChem Extensions For KNIME - ChemAxon

JChem Extensions for KNIMEAaron HartKNIME.com AG

The KNIME Platform

KNIME Product PortfolioKNIME Cluster Cluster Execution Advanced HardwareUtilizationKNIME Server All KNIME Team Space FeaturesServer BasedRemote ExecutionScheduled ExecutionWeb Portal: WorkflowsWeb ServiceUser AuthenticationUser Rights ManagementKNIMETeam Space KNIMEProfessionalKNIME AutomatedWeb IntegratedManagedSecureAll KNIME Professional FeaturesShared Workflow RepositoryShared Data SpaceShared Metanodes MaintainableShareable All KNIME FeaturesCommercial AgreementProfessional SupportPriority Development Professional AccessTransformationStatisticsData MiningVisualizationReportingInteractive / Batch ExecutionWorkflow Interface Full FunctionOpen SourceExtendable3rd PartyIntegrationScalable

KNIME Core Chemistry IO Mining Fingerprint Bayesian learner/predictor MoSS & Moss MCSS similarity SDF Property extraction and InsertionMiscTranslators Molecule Type Cast converts strings to native KNIMEchemistry types OpenBabel translates between chemistry typesMarvin Readers and writers for Mol2, Mol, Rxn, SDF and Smiles.Sketch, Convert and View (2d and 3d)Others Distance matrix, Similarity Search

KNIME Core Chemistry IINew Features in 2.7:Fingerprint Bayesian Modeling Predict activity based onmolecular fingerprintsSimilarity Search Find molecules similar to query

KNIME CommunityCheminformatics Contributions– RDKit Chemoinformatics library (supported by Novartis)– Indigo Chemoinformatics library (GGA Software)– Erlwood Chemoinformatics Collection of nodes geared towards pharmaceuticalresearch (Eli-Lilly)– CDK Integration of the well-known Java library for structuralchemo-and bioinformatics (EBI)Others In Bioinformatics, Scripting, Information Retrieval

Technology Partners– only Life Sciences – ChemAxon / InfocomChemical Computing GroupSchrödingerCressetTriposBioSolve http://www.knime.org/files/molegro logo.pngITSpotfireMolecular DiscoveryTrewerenKorilogMolegro

JChem Extensions Extensions of ChemAxon’s tool for KNIMEworkflow Infocom implement it with the supportof ChemAxon Contains over 90% of ChemAxon'scheminformatics functionality

Marvin Family Nodes––––Marvin SketchMarvin ViewMarvin SpaceConverterAvailable as part of KNIME’s core chemistry extensionsFree of charge for ALL customers!!

Document to Structure Extracts names from textdocuments (Text, PDF and HTML)Structure images are alsoconvertedAutomatic text OCRAlso import smiles, InChI and CASnumberSupport the common officedocument formats (It’s new!)

Markush Structures ture generationViewer

JChem for ExcelJC4XL Reader– Reads Excel file created withJChem For Excel.JC4XL Writer– Writes JChem For Excelcompatible xlsx file.

Come to therd3KNIME Life Science DayChemistry in KNIME WebinarMeet the KNIME people and other customersHear aboutLife Sciences applicationswww.knime.org/events(or comespeak with contributionsus!)Get to knowcommunityListen to partner presentationsat theSketch with MarvinCalculate MolecularthDescriptorsThis Friday (28 )Read/Write Chemistry data typesNERD center in Cambridge, MAGet structures from ChEMBL

KNIME Core Chemistry IO Readers and writers for Mol2, Mol, Rxn, SDF and Smiles. Mining Fingerprint Bayesian learner/predictor MoSS & Moss MCSS similarity Misc SDF Property extraction and Insertion Translators Molecule Type Cast converts