AIMC Topic: Ligands

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Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference.

Journal of chemical information and modeling Mar 23, 2021
Predicting accurate protein-ligand binding affinities is an important task in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite th...
Protein Binding Proteins Ligands Neural Networks, Computer Software
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Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein-Ligand Binding Affinity Prediction.

Journal of chemical information and modeling Mar 16, 2021
Efficient molecular featurization is one of the major issues for machine learning models in drug design. Here, we propose a persistent Ricci curvature (PRC), in particular, Ollivier PRC (OPRC), for the molecular featurization and feature engineering,...
Ligands Proteins Databases, Protein Machine Learning Protein Binding
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Target2DeNovoDrug: a novel programmatic tool for -deep learning based drug design for any target of interest.

Journal of biomolecular structure & dynamics Mar 11, 2021
The on-going data-science and Artificial Intelligence (AI) revolution offer researchers a fresh set of tools to approach structure-based drug design problems in the computer-aided drug design space. A novel programmatic tool that incorporates and de...
Artificial Intelligence Molecular Dynamics Simulation Ligands Drug Design Deep Learning
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Expanding the drug discovery space with predicted metabolite-target interactions.

Communications biology Mar 5, 2021
Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potenti...
Humans Metabolomics Drug Discovery Metabolome Gene Expression Profiling Databases, Factual Anti-Inflammatory Agents Ligands Protein Interaction Maps Inflammatory Bowel Diseases Molecular Targeted Therapy Bacteria Transcriptome Machine Learning Signal Transduction Host-Pathogen Interactions Cells, Cultured Gastrointestinal Agents Gastrointestinal Microbiome Data Mining
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Trends in application of advancing computational approaches in GPCR ligand discovery.

Experimental biology and medicine (Maywood, N.J.) Feb 27, 2021
G protein-coupled receptors (GPCRs) comprise the most important superfamily of protein targets in current ligand discovery and drug development. GPCRs are integral membrane proteins that play key roles in various cellular signaling processes. Therefo...
Machine Learning Drug Design Receptors, G-Protein-Coupled Ligands Drug Discovery Humans
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Androgen Receptor Binding Category Prediction with Deep Neural Networks and Structure-, Ligand-, and Statistically Based Features.

Molecules (Basel, Switzerland) Feb 26, 2021
Substances that can modify the androgen receptor pathway in humans and animals are entering the environment and food chain with the proven ability to disrupt hormonal systems and leading to toxicity and adverse effects on reproduction, brain developm...
Receptors, Androgen Proteins Software Ligands Algorithms Humans Neural Networks, Computer Protein Binding Animals Logistic Models Deep Learning Rats
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Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment.

Journal of chemical information and modeling Feb 25, 2021
Graph neural networks are able to solve certain drug discovery tasks such as molecular property prediction and molecule generation. However, these models are considered "black-box" and "hard-to-debug". This study aimed to improve modeling transparen...
Artificial Intelligence Drug Discovery Ligands Neural Networks, Computer
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Role of Soluble T-Cell Immunoglobulin Mucin Domain-3 in Differentiating Nontuberculous Mycobacterial Lung Disease from Pulmonary Colonization.

Archivos de bronconeumologia Feb 24, 2021
BACKGROUND: Differentiating between nontuberculous mycobacterial lung disease (NTM-LD) and pulmonary NTM colonization (NTM-Col) is difficult. Compared with healthy controls, patients with NTM-LD generally present immune tolerance along with increased...
Immunoglobulins Ligands Pneumonia Humans Mucins Mycobacterium Infections, Nontuberculous Hepatitis A Virus Cellular Receptor 2 T-Lymphocytes Programmed Cell Death 1 Receptor
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Machine learning classifiers aid virtual screening for efficient design of mini-protein therapeutics.

Bioorganic & medicinal chemistry letters Feb 18, 2021
De novo design of mini-proteins (4-12 kDa) has recently been shown to produce new candidates for protein therapeutics. They are temperature stable molecules that bind to the drug target with high affinity for inhibiting its interactions. The developm...
Ligands Small Molecule Libraries Machine Learning Proteins
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OctSurf: Efficient hierarchical voxel-based molecular surface representation for protein-ligand affinity prediction.

Journal of molecular graphics & modelling Feb 9, 2021
Voxel-based 3D convolutional neural networks (CNNs) have been applied to predict protein-ligand binding affinity. However, the memory usage and computation cost of these voxel-based approaches increase cubically with respect to spatial resolution and...
Proteins Ligands Neural Networks, Computer Protein Binding
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