AIMC Topic: Ligands

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Computational representations of protein-ligand interfaces for structure-based virtual screening.

Expert opinion on drug discovery Jun 3, 2021
: Structure-based virtual screening (SBVS) is an essential strategy for hit identification. SBVS primarily uses molecular docking, which exploits the protein-ligand binding mode and associated affinity score for compound ranking. Previous studies hav...
Humans Protein Binding Proteins Ligands Machine Learning Molecular Docking Simulation
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Deep Scoring Neural Network Replacing the Scoring Function Components to Improve the Performance of Structure-Based Molecular Docking.

ACS chemical neuroscience Jun 3, 2021
Accurate prediction of protein-ligand interactions can greatly promote drug development. Recently, a number of deep-learning-based methods have been proposed to predict protein-ligand binding affinities. However, these methods independently extract t...
Ligands Protein Binding Proteins Neural Networks, Computer Molecular Docking Simulation
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VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization.

International journal of molecular sciences May 28, 2021
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and th...
Kelch-Like ECH-Associated Protein 1 Protein Binding NF-E2-Related Factor 2 Artificial Intelligence Reproducibility of Results Ligands Computational Biology Algorithms Thermodynamics Molecular Docking Simulation Protein Conformation
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Recent progress on the prospective application of machine learning to structure-based virtual screening.

Current opinion in chemical biology May 27, 2021
As more bioactivity and protein structure data become available, scoring functions (SFs) using machine learning (ML) to leverage these data sets continue to gain further accuracy and broader applicability. Advances in our understanding of the optimal...
Machine Learning Ligands Molecular Docking Simulation Proteins
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DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization.

Journal of chemical information and modeling May 24, 2021
Lead optimization, a critical step in early stage drug discovery, involves making chemical modifications to a small-molecule ligand to improve properties such as binding affinity. We recently developed DeepFrag, a deep-learning model capable of recom...
Deep Learning Internet Software Mobile Applications Ligands Computers Web Browser Humans
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ET-score: Improving Protein-ligand Binding Affinity Prediction Based on Distance-weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm.

Molecular informatics May 21, 2021
The molecular docking simulation is a key computational tool in modern drug discovery research that its predictive performance strongly depends on the employed scoring functions. Many recent studies have shown that the application of machine learning...
Ligands Protein Binding Proteins Machine Learning Molecular Docking Simulation
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Ligand-Dependent Conformational Transitions in Molecular Dynamics Trajectories of GPCRs Revealed by a New Machine Learning Rare Event Detection Protocol.

Molecules (Basel, Switzerland) May 20, 2021
Central among the tools and approaches used for ligand discovery and design are Molecular Dynamics (MD) simulations, which follow the dynamic changes in molecular structure in response to the environmental condition, interactions with other proteins,...
Humans Machine Learning Ligands Receptors, G-Protein-Coupled Protein Conformation Molecular Dynamics Simulation
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DeepBSP-a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures.

Journal of chemical information and modeling May 12, 2021
In recent years, machine-learning-based scoring functions have significantly improved the scoring power. However, many of these methods do not perform well in distinguishing the native structure from docked decoy poses due to the lack of decoy struct...
Machine Learning Proteins Ligands Molecular Docking Simulation Protein Binding
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An Integrated Approach toward NanoBRET Tracers for Analysis of GPCR Ligand Engagement.

Molecules (Basel, Switzerland) May 12, 2021
Gaining insight into the pharmacology of ligand engagement with G-protein coupled receptors (GPCRs) under biologically relevant conditions is vital to both drug discovery and basic research. NanoLuc-based bioluminescence resonance energy transfer (Na...
Luminescent Agents Binding, Competitive Bioluminescence Resonance Energy Transfer Techniques Ligands HEK293 Cells Humans Luciferases Transfection Drug Discovery Protein Binding Receptors, G-Protein-Coupled Machine Learning Molecular Docking Simulation
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Integrated support vector machine and pharmacophore based virtual screening driven identification of thiophene carboxamide scaffold containing compound as potential PARP1 inhibitor.

Journal of biomolecular structure & dynamics May 5, 2021
Poly (ADP-ribose) polymerase-1 (PARP1) inhibition strategy for cancer treatment is gaining advantage particularly in patients having a mutation in BRCA1/BRCA2 gene. To date, four drugs have obtained FDA approval and some inhibitors are in clinical tr...
Humans Thiophenes Quantitative Structure-Activity Relationship Poly (ADP-Ribose) Polymerase-1 Molecular Dynamics Simulation Molecular Docking Simulation Ligands Support Vector Machine
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