Evidence
J Chem Inf Model. 2024 Jun 13. doi: 10.1021/acs.jcim.4c00031. Online ahead of print.
ABSTRACT
Optimization techniques play a pivotal role in advancing drug development, serving as the foundation of numerous generative methods tailored to efficiently design optimized molecules derived from existing lead compounds. However, existing methods often encounter difficulties in generating diverse, novel, and high-property molecules that simultaneously optimize multiple drug properties. To overcome this bottleneck, we propose a multiobjective molecule optimization framework (MOMO). MOMO employs a specially designed Pareto-based multiproperty evaluation strategy at the molecular sequence level to guide the evolutionary search in an implicit chemical space. A comparative analysis of MOMO with five state-of-the-art methods across two benchmark multiproperty molecule optimization tasks reveals that MOMO markedly outperforms them in terms of diversity, novelty, and optimized properties. The practical applicability of MOMO in drug discovery has also been validated on four challenging tasks in the real-world discovery problem. These results suggest that MOMO can provide a useful tool to facilitate molecule optimization problems with multiple properties.
PMID:38870455 | DOI:10.1021/acs.jcim.4c00031
Estimated reading time: 3 minute(s)
Latest: Psychiatryai.com #RAISR4D Evidence
Cool Evidence: Engaging Young People and Students in Real-World Evidence
Real-Time Evidence Search [Psychiatry]
AI Research
Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space
🌐 90 Days
AI Virtual Reality Related Evidence Matrix
- Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space
- Accelerating Molecular Docking using Machine Learning Methods
- Generative Artificial Intelligence for Designing Multi-Scale Hydrogen Fuel Cell Catalyst Layer Nanostructures
- SDDSynergy: Learning Important Molecular Substructures for Explainable Anticancer Drug Synergy Prediction
- Discovery of Potent Multikinase Type-II Inhibitors Targeting CDK5 in the DFG-out Inactive State with Promising Potential against Glioblastoma
- Revolutionizing Playing with Skeleton Atoms: Molecular Editing Surgery in Medicinal Chemistry
- Emerging opportunities of using large language models for translation between drug molecules and indications
- OpenChemIE: An Information Extraction Toolkit for Chemistry Literature
- Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction
- HydrogelFinder: A Foundation Model for Efficient Self-Assembling Peptide Discovery Guided by Non-Peptidal Small Molecules
- Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model
- Deep Learning Bridged Bioactivity, Structure, and GC-HRMS-Readable Evidence to Decipher Nontarget Toxicants in Sediments
- Discovery of 3-((4-Benzylpyridin-2-yl)amino)benzamides as Potent GPR52 G Protein-Biased Agonists
- A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation
- Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives
- Combining Bayesian optimization and automation to simultaneously optimize reaction conditions and routes
- Accelerating Computation of Acidity Constants and Redox Potentials for Aqueous Organic Redox Flow Batteries by Machine Learning Potential-Based Molecular Dynamics
- mRNA-CLA: An Interpretable Deep Learning Approach for Predicting mRNA Subcellular Localization
- Fentanyl-Type Antagonist of the μ-Opioid Receptor: Important Role of Axial Chirality in the Active Conformation
- The Role of AI in Drug Discovery
- In Silico Chemical Experiments in the Age of AI: From Quantum Chemistry to Machine Learning and Back
- Modulating a model membrane of sphingomyelin by a tricyclic antidepressant drug
- PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models
- Discovery of New Phenyltetrazolium Derivatives as Ferroptosis Inhibitors for Treating Ischemic Stroke: An Example Development from Free Radical Scavengers
- Predicting blood-brain barrier permeability of molecules with a large language model and machine learning
- Bohemian Rhapsody of Future Drug Delivery Systems: Rational Changes Necessary for the Next Revolution
- CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space
- Identification of Anticancer Peptides from the Genome of Candida albicans: in Silico Screening, in Vitro and in Vivo Validations
- Label-free detection and profiling of individual solution-phase molecules
- Label-free detection and profiling of individual solution-phase molecules
- Improved Latin hypercube sampling initialization-based whale optimization algorithm for COVID-19 X-ray multi-threshold image segmentation
- Mapping of specialized metabolite terms onto a plant phylogeny using text mining and large language models
- Acquired Capability for Suicide: An Evolutionary Concept Analysis
- TriKSV-LG: a robust approach to disease prediction in healthcare systems using AI and Levy Gazelle optimization
- A theoretical study of the oxidation of benzene by manganese oxide clusters: formation of quinone intermediates
- Improved Molecular Packing of Self-Assembled Monolayer Charge Injectors for Perovskite Light-Emitting Diodes
- Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment
- An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model
- Designing combinational herbal drugs based on target space analysis
- Development of an alcoholic liver disease model for drug evaluation from human induced pluripotent stem cell-derived liver organoids
- Development of an alcoholic liver disease model for drug evaluation from human induced pluripotent stem cell-derived liver organoids
- Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution
- Molecular modeling of multi-target analogs of huperzine A and applications in Alzheimer's disease
- Deep generative spatiotemporal learning for integrating fracture mechanics in composite materials: inverse design, discovery, and optimization
- The Benzoylpiperidine Fragment as a Privileged Structure in Medicinal Chemistry: A Comprehensive Review
- The Benzoylpiperidine Fragment as a Privileged Structure in Medicinal Chemistry: A Comprehensive Review
- High-Efficiency Effect-Directed Analysis Leveraging Five High Level Advancements: A Critical Review
- Improving the Biocompatibility and Functionality of Neural Interface Devices with Silica Nanoparticles
- Improved Imaging Surface for Quantitative Single-Molecule Microscopy
- Development of Peptide-Based Probes for Molecular Imaging of the Postsynaptic Density in the Brain
- RevGraphVAMP: A protein molecular simulation analysis model combining graph convolutional neural networks and physical constraints
- MIFAM-DTI: a drug-target interactions predicting model based on multi-source information fusion and attention mechanism
- Sharing massive biomedical data at magnitudes lower bandwidth using implicit neural function
- Predicting Emission of Heteroleptic Iridium Complexes using Artificial Chemical Intelligence
- Discovery of a Highly Potent and Selective BRD9 PROTAC Degrader Based on E3 Binder Investigation for the Treatment of Hematological Tumors
- Impact of Sacrificial Hydrogen Bonds on the Structure and Properties of Rubber Materials: Insights from All-Atom Molecular Dynamics Simulations
- A Second Space Age Spanning Omics, Platforms, and Medicine Across Orbits
- Enhancing hERG Risk Assessment with Interpretable Classificatory and Regression Models
- Enhancing the Efficiency and Stability of Inverted Formamidinium-Cesium Lead-Triiodide Perovskite Solar Cells through Lewis Base Pretreatment of Buried Interfaces
- Design and Synthesis of Clinical Candidate PF-06852231 (CVL-231): A Brain Penetrant, Selective, Positive Allosteric Modulator of the M4 Muscarinic Acetylcholine Receptor
- SuFEx-Enabled Direct Deoxy-Diversification of Alcohols
- AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences
- Application of Deep Learning for Studying NMDA Receptors
- Small-Molecule Inhibitors of TIPE3 Protein Identified through Deep Learning Suppress Cancer Cell Growth In Vitro
Evidence Blueprint
Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space
☊ AI-Driven Related Evidence Nodes
(recent articles with at least 5 words in title)
More Evidence
Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space
🌐 365 Days
AI Virtual Reality Related Evidence Matrix
- Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space
- MolProphet: A One-Stop, General Purpose, and AI-Based Platform for the Early Stages of Drug Discovery
- Accelerating Molecular Docking using Machine Learning Methods
- Generative Artificial Intelligence for Designing Multi-Scale Hydrogen Fuel Cell Catalyst Layer Nanostructures
- SDDSynergy: Learning Important Molecular Substructures for Explainable Anticancer Drug Synergy Prediction
- MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning
- Discovery of Potent Multikinase Type-II Inhibitors Targeting CDK5 in the DFG-out Inactive State with Promising Potential against Glioblastoma
- Revolutionizing Playing with Skeleton Atoms: Molecular Editing Surgery in Medicinal Chemistry
- Emerging opportunities of using large language models for translation between drug molecules and indications
- OpenChemIE: An Information Extraction Toolkit for Chemistry Literature
- Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction
- HydrogelFinder: A Foundation Model for Efficient Self-Assembling Peptide Discovery Guided by Non-Peptidal Small Molecules
- Protein Engineering with Lightweight Graph Denoising Neural Networks
- Is Target-Based Drug Discovery Efficient? Discovery and "Off-Target" Mechanisms of All Drugs
- Single-Molecule-Resolution Approaches in Synaptic Biology
- Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model
- Development of Novel Methods for QSAR Modeling by Machine Learning Repeatedly: A Case Study on Drug Distribution to Each Tissue
- Deep Learning Bridged Bioactivity, Structure, and GC-HRMS-Readable Evidence to Decipher Nontarget Toxicants in Sediments
- Discovery of 3-((4-Benzylpyridin-2-yl)amino)benzamides as Potent GPR52 G Protein-Biased Agonists
- A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation
- Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives
- Novel Substituted Pyrimidine Derivatives as Potential Anti-Alzheimer's Agents: Synthesis, Biological, and Molecular Docking Studies
- How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?
- RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding
- Combining Bayesian optimization and automation to simultaneously optimize reaction conditions and routes
- Accelerating Computation of Acidity Constants and Redox Potentials for Aqueous Organic Redox Flow Batteries by Machine Learning Potential-Based Molecular Dynamics
- A Combin aed Ligand- and Structure-Based Virtual Screening To Identify Novel NaV1.2 Blockers: In Vitro Patch Clamp Validation and In Vivo Anticonvulsant Activity
- mRNA-CLA: An Interpretable Deep Learning Approach for Predicting mRNA Subcellular Localization
- Recent Advances in Fluorescent Theranostics for Alzheimer's Disease: A Comprehensive Survey on Design, Synthesis, and Properties
- Fentanyl-Type Antagonist of the μ-Opioid Receptor: Important Role of Axial Chirality in the Active Conformation
- Infrared Spectroscopy for Rapid Triage of Cancer Using Blood Derivatives: A Reality Check
- The Role of AI in Drug Discovery
- In Silico Chemical Experiments in the Age of AI: From Quantum Chemistry to Machine Learning and Back
- Analysis of COVID-19 severity from the perspective of coagulation index using evolutionary machine learning with enhanced brain storm optimization
- Modulating a model membrane of sphingomyelin by a tricyclic antidepressant drug
- Kinome-Wide Virtual Screening by Multi-Task Deep Learning
- PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models
- Discovery of New Phenyltetrazolium Derivatives as Ferroptosis Inhibitors for Treating Ischemic Stroke: An Example Development from Free Radical Scavengers
- Predicting blood-brain barrier permeability of molecules with a large language model and machine learning
- Bohemian Rhapsody of Future Drug Delivery Systems: Rational Changes Necessary for the Next Revolution
- CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space
- Identification of Anticancer Peptides from the Genome of Candida albicans: in Silico Screening, in Vitro and in Vivo Validations
- Atomic Force Microscopy beyond Topography: Chemical Sensing of 2D Material Surfaces through Adhesion Measurements
- Label-free detection and profiling of individual solution-phase molecules
- Label-free detection and profiling of individual solution-phase molecules
- Improved Latin hypercube sampling initialization-based whale optimization algorithm for COVID-19 X-ray multi-threshold image segmentation
- Potential Mechanisms Involving in the Pathogenesis of MASLD and Targets for Pharmacotherapy. Advancements in Metabolic Associated Steatotic Liver Disease (MASLD) Research: Diagnostics, Small Molecule Developments and Future Directions
- Mapping of specialized metabolite terms onto a plant phylogeny using text mining and large language models
- Acquired Capability for Suicide: An Evolutionary Concept Analysis
- Differentiating the Yield of Chemical Reactions Using Parameters in First-Order Kinetic Equations to Identify Elementary Steps That Control the Reactivity from Complicated Reaction Path Networks
- Enhancing drug discovery in schizophrenia: a deep learning approach for accurate drug-target interaction prediction - DrugSchizoNet
- Enhancing drug discovery in schizophrenia: a deep learning approach for accurate drug-target interaction prediction - DrugSchizoNet
- Amyloid Targeting Red Emitting AIE Dots for Diagnostic and Therapeutic Application against Alzheimer's Disease
- Kinome-Wide Virtual Screening by Multi-Task Deep Learning
- TriKSV-LG: a robust approach to disease prediction in healthcare systems using AI and Levy Gazelle optimization
- A theoretical study of the oxidation of benzene by manganese oxide clusters: formation of quinone intermediates
- Improved Molecular Packing of Self-Assembled Monolayer Charge Injectors for Perovskite Light-Emitting Diodes
- Crystallographic mining driven computer-guided approach to identify the ASK1 inhibitor likely to perturb the catalytic region
- Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment
- An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model
- Binding-Free Taste Visualization with Plasmonic Metasurfaces
- MFTrans: A multi-feature transformer network for protein secondary structure prediction
- Designing combinational herbal drugs based on target space analysis
- Development of an alcoholic liver disease model for drug evaluation from human induced pluripotent stem cell-derived liver organoids