14.-MOE-Course-KNIME-Interface-Introduction

Copyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEMOEExtensionsforKNIMEVersion2.0.0Copyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEChemicalComputingGroup▪CCG'stwomainproducts–MolecularOperatingEnvironmentTM–PSILO®–ProteinSilo▪CCG'sstrengths–LeadingscientificR&DgroupinCAMD–Collaborativecustomersupport–Highqualitysoftwareengineering▪14+yearsofconsistentinnovationandproductreleasesScientificLiteratureCitationsofMOE050100150200250300350400450500CCGfoundedin1994•Lifesciencessoftwarecompany•HeadquartersinMontreal/Canada•Offices:UK,Germany•800+customersworldwideMolecularOperatingEnvironment™•PharmacophoreDiscovery•Structure-BasedDrugDesign•ProteinandAntibodyModeling•MolecularModelingandSimulations•Cheminformaticsand(HTS)QSAR•MedicinalChemistryApplications•MethodsDevelopment&DeploymentCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEMOE:CommonPlatformforDifferentResearchGroupsPharmacophoreDiscoveryProteinModelingMethodologyDevelopmentStructureBasedDrugDesignModelingandSimulationsQSAR/HTSCheminformaticsMOEMOE/batch•MOE/smpMOE/web•MOE/javaMedicinalChemistsComputationalExpertsOccasionalUsersClusterNodeClusterNodeClusterNodeClusterNodeDesktop•Cluster•PipelineWorkflowWindows•Linux•Unix•BrowserOEBClipboardFlatFileIntranetOracleSocketLocalFiles•Cut&PasteMOE/javaSystemforConnectivityCheminformaticiansCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOESVL:Built-InProgrammingLanguageofMOEMOEisbuiltwithachemistry-awareembeddedlanguageSVLisaportablehigh-levellanguageApplications/scriptsarewritteninSVL–sourcecodeisshippedTheMolecularOperatingEnvironment(MOE)CustomSVLApplicationsCoreInterfaceInterfaceToolkitPortabilityLayerMolecularToolsOperatingSystemGraphicsSystemAPIBaseSystem(C)Applications(SVL)SVLLibrariesCCGApplicationsTheScientificVectorLanguage(SVL)PlatformIndependenceSVLandthePortabilityLayereliminatedependenciesonhardwareandoperatingsystem.ApplicationProgramInterfaceIn-houseorexternalcodelibrariescanbeincorporatedtoextendthebuilt-infunctionality.Copyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOE0102030405060708090MOENodesMOEExtensions:ASuccessStory▪Activedevelopmentsince2007▪Customerdrivennodedevelopment▪KNIMEPartnerssince20111.1.2CustomPackages1.1.4Mol2Cell1.1.6NDK1.1.8MOEPorts1.2.0Copyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEMOEExtensions:FactsandBenefits▪CCGofferingsforKNIME–80+pre-builtMOEnodesincluded–OpenSVLandJavasourcecode–Addyourownextensions–TestedwithMOE2010.10–TestedwithKNIME2.3.1▪SupportedbyCCG–InstructionsavailableontheSVLExchange–Mailinglistforupdates–Comprehensivedocumentation▪AvailablefreeofchargetoMOEUsersSubcategoriesinMOENodeRepositoryCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEKNIMENodesPoweredbyMOE/batch▪Two-LayerArchitecture–EnsuresidenticalresultsasinMOE/batch–SVLfilescanbeeditedindependently▪JavaLayercontrolsIn-andOutput–MOEusedforchemistrycalculationsonly–Efficientlicensetokenusage–CommunicationrevisedforspeedSVLLayerInputOutputJavaLayerNODEGeneratesJavaLayerfromSVLCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOECCGNodeDevelopment▪NodesforMOEApplications–Synthetic'feasibility'(rsynth)–Protonate3Dforproteinpreparation▪NodesforSVLExchange/SupportApplications–ReadIsisDrawSketchFiles–ShannonEntropyModel▪NodesforApplicationsrequestedbyUsers–MurckoFramework–WritePharmacophoreModel–CATSCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEAvailableMOENodesThecurrentsetofnodescoversthewholefieldoflife-scienceresearch.Copyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOECompileMOE/batchSVLintoKNIMENodes▪User-friendlygraphicalinterfaceforcross-compilation–Javabased(SunJDKrequired)–Windows,LinuxandMacOSXsupported–Eclipseinstallationnotrequired▪CreatecustomMOE-basedextensions–CompilenewnodesfromSVLsources–Sharenodeswithothers–SVLtemplatesprovided–Functiondocumentationavailable▪Managemultipleextensions–Modulararchitecture–FoldersareinterpretedasseparatepackagesCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEChemistryTypesforSmallandLargeMoleculesSdfCell,MolCell,CtabCell:DrugsizeMoleculesV2000isawidelysupportedstandard999atomslimitLackspartialchargesMol2Cell:LargeMolecules(TriposMOL2Format)NohardcodedatomlimitPartialchargesaresupportedNon-standardDesignshouldallowtoavoidunnecessaryconverternodesAlltypesofmoleculescanbehandledV3000issupportedbyMOE,butnotastandardelsewhereCopyright©2011ChemicalComputingGroupInc.AllRightsReserved.MolecularOperatingEnvironmentMOEMOEModelPorts▪SpecialMOEModelPortsguidevisualnodeconnections–ConnecttootherMOEModelPorts–ConnecttogenericKNIMEModelPorts▪UsedforvarietyofMOEbasedmodels–QSAR–Fingerprint–Compositemodels–…▪Removeambiguitywhenconnec