2024
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations
Tang X, Tran A, Tan J, Gerstein M. MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. Bioinformatics 2024, 40: i357-i368. PMID: 38940177, PMCID: PMC11256921, DOI: 10.1093/bioinformatics/btae260.Peer-Reviewed Original ResearchConceptsTransformer encoderDownstream tasksLanguage modelBiomedical textSelf-supervised pre-trainingExplicit 3D representationRepresentation improves performanceDeep learning modelsRepresentation of moleculesContrastive learningSupervisory signalExtract embeddingsRepresentation capabilityJoint representationBiomedical domainPre-trainingTextual dataLearning modelsMolecular representationsModel weightsJupyter NotebookStep-by-step guidanceEncodingProperty predictionStructural information
2023
Chemical representation learning for toxicity prediction
Born J, Markert G, Janakarajan N, Kimber T, Volkamer A, Martínez M, Manica M. Chemical representation learning for toxicity prediction. Digital Discovery 2023, 2: 674-691. DOI: 10.1039/d2dd00099g.Peer-Reviewed Original ResearchChemical language modelsLanguage modelMolecular property prediction tasksMolecular property prediction modelProperty prediction tasksMolecular property predictionExplicit supervisionAttention weightsMultiscale convolutionData augmentationPrediction taskToxicity datasetMolecular representationsProperty prediction modelsImproved accuracyModel reliabilityDatasetProperty predictionChemical representationsToxicity predictionPrediction uncertaintyUncertainty estimationDrug discoveryRepresentationPrediction model
2004
Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions
Soudackov A, Hatcher E, Hammes-Schiffer S. Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions. The Journal Of Chemical Physics 2004, 122: 014505. PMID: 15638672, DOI: 10.1063/1.1814635.Peer-Reviewed Original ResearchConceptsElectron transfer reactionsTransfer reactionsMultistate valence bond modelProton donor-acceptor vibrational motionProton donor-acceptor distanceValence bond modelDonor-acceptor distanceRate expressionNonadiabatic rate expressionMolecular dynamics simulationsPCET reactionsPCET systemsNonadiabatic protonDielectric continuum modelDielectric continuumMolecular representationsDynamics simulationsVibrational modesVibrational motionActive electronsReactionBond modelQuantum mechanical treatmentProtonsContinuum model
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