AIMC Journal:
Journal of chemical information and modeling

Showing 311 to 320 of 934 articles

Directional Δ Neural Network (DrΔ-Net): A Modular Neural Network Approach to Binding Free Energy Prediction.

Journal of chemical information and modeling Mar 12, 2024
The protein-ligand binding free energy is a central quantity in structure-based computational drug discovery efforts. Although popular alchemical methods provide sound statistical means of computing the binding free energy of a large breadth of syste...
Ligands Proteins Entropy Protein Binding Neural Networks, Computer
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DeePNAP: A Deep Learning Method to Predict Protein-Nucleic Acid Binding Affinity from Their Sequences.

Journal of chemical information and modeling Mar 8, 2024
Predicting the protein-nucleic acid (PNA) binding affinity solely from their sequences is of paramount importance for the experimental design and analysis of PNA interactions (PNAIs). A large number of currently developed models for binding affinity ...
Nucleic Acids Proteins Mutation Protein Binding Deep Learning
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Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations.

Journal of chemical information and modeling Mar 8, 2024
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that mediates biological signals to control various complicated cellular functions. It plays a crucial role in environmental sensing and xenobiotic metabolism. Dysregulati...
Ligands Aryl Hydrocarbon Receptor Nuclear Translocator Receptors, Aryl Hydrocarbon Artificial Intelligence Humans
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Coarse-Grained Crystal Graph Neural Networks for Reticular Materials Design.

Journal of chemical information and modeling Mar 8, 2024
Reticular materials, including metal-organic frameworks and covalent organic frameworks, combine the relative ease of synthesis and an impressive range of applications in various fields from gas storage to biomedicine. Diverse properties arise from t...
Algorithms Research Design Artificial Intelligence Neural Networks, Computer Metal-Organic Frameworks
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Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction.

Journal of chemical information and modeling Mar 6, 2024
Active learning (AL) has become a powerful tool in computational drug discovery, enabling the identification of top binders from vast molecular libraries. To design a robust AL protocol, it is important to understand the influence of AL parameters, a...
Ligands Machine Learning Drug Discovery
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Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning.

Journal of chemical information and modeling Mar 5, 2024
Improving the generalization ability of scoring functions remains a major challenge in protein-ligand binding affinity prediction. Many machine learning methods are limited by their reliance on single-modal representations, hindering a comprehensive ...
Ligands Neural Networks, Computer Mutation Drug Discovery Machine Learning
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Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers.

Journal of chemical information and modeling Mar 1, 2024
Multiscale modeling of complex molecular systems, such as macromolecules, encompasses methods that combine information from fine and coarse representations of molecules to capture material properties over a wide range of spatiotemporal scales. Being ...
Deep Learning Stereoisomerism Physics Polyesters Polymers
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Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques.

Journal of chemical information and modeling Feb 29, 2024
The world has witnessed a revolution in therapeutics with the development of biological medicines such as antibodies and antibody fragments, notably nanobodies. These nanobodies possess unique characteristics including high specificity and modulatory...
Single-Domain Antibodies Deep Learning Receptor, Metabotropic Glutamate 5 Molecular Dynamics Simulation Models, Molecular Animals Protein Conformation Epitope Mapping Rats Epitopes
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Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks.

Journal of chemical information and modeling Feb 29, 2024
Molecular design depends heavily on optical properties for applications such as solar cells and polymer-based batteries. Accurate prediction of these properties is essential, and multiple predictive methods exist, from to data-driven techniques. Alt...
Machine Learning Density Functional Theory Spectrum Analysis Neural Networks, Computer Bayes Theorem
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PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery.

Journal of chemical information and modeling Feb 25, 2024
PandaOmics is a cloud-based software platform that applies artificial intelligence and bioinformatics techniques to multimodal omics and biomedical text data for therapeutic target and biomarker discovery. PandaOmics generates novel and repurposed th...
Software Artificial Intelligence Drug Discovery Biomarkers Humans Computational Biology
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