AIMC Topic: Ligands

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Integrated Molecular Modeling and Machine Learning for Drug Design.

Journal of chemical theory and computation Oct 26, 2023
Modern therapeutic development often involves several stages that are interconnected, and multiple iterations are usually required to bring a new drug to the market. Computational approaches have increasingly become an indispensable part of helping r...
Ligands Drug Design Retrospective Studies Machine Learning Molecular Docking Simulation Proteins
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Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets.

Journal of chemical information and modeling Oct 26, 2023
Small-molecule conformer generation (SMCG) is an extremely important task in both ligand- and structure-based computer-aided drug design, especially during the hit discovery phase. Recently, a multitude of artificial intelligence (AI) models tailored...
Ligands Molecular Conformation Artificial Intelligence Drug Design Models, Molecular
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CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces.

Proteins Oct 23, 2023
Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted...
Ligands Protein Conformation Databases, Protein Models, Molecular Protein Interaction Domains and Motifs Binding Sites Protein Interaction Mapping Deep Learning Protein Binding Computational Biology Proteins Humans Software
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Ensemble of local and global information for Protein-Ligand Binding Affinity Prediction.

Computational biology and chemistry Oct 20, 2023
Accurately predicting protein-ligand binding affinities is crucial for determining molecular properties and understanding their physical effects. Neural networks and transformers are the predominant methods for sequence modeling, and both have been s...
Protein Binding Proteins Ligands Neural Networks, Computer Algorithms
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A practical guide to machine-learning scoring for structure-based virtual screening.

Nature protocols Oct 16, 2023
Structure-based virtual screening (SBVS) via docking has been used to discover active molecules for a range of therapeutic targets. Chemical and protein data sets that contain integrated bioactivity information have increased both in number and in si...
Acetylcholinesterase Molecular Docking Simulation Ligands Artificial Intelligence Machine Learning Algorithms
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Graph neural networks for the identification of novel inhibitors of a small RNA.

SLAS discovery : advancing life sciences R & D Oct 14, 2023
MicroRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation and have been implicated in various diseases, including cancers and lung disease. In recent years, Graph Neural Networks (GNNs) have emerged as powerful tools for analyzin...
Neural Networks, Computer Ligands Small Molecule Libraries MicroRNAs Molecular Structure
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Epigenetic target identification strategy based on multi-feature learning.

Journal of biomolecular structure & dynamics Oct 12, 2023
The identification of potential epigenetic targets for a known bioactive compound is essential and promising as more and more epigenetic drugs are used in cancer clinical treatment and the availability of chemogenomic data related to epigenetics incr...
Ligands Neural Networks, Computer Epigenesis, Genetic Machine Learning Drug Discovery Humans Algorithms Epigenomics Protein Binding Molecular Docking Simulation
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ResBiGAAT: Residual Bi-GRU with attention for protein-ligand binding affinity prediction.

Computational biology and chemistry Oct 11, 2023
Protein-ligand interaction plays a crucial role in drug discovery, facilitating efficient drug development and enabling drug repurposing. Several computational algorithms, such as Graph Neural Networks and Convolutional Neural Networks, have been pro...
Neural Networks, Computer Ligands Protein Binding Algorithms Proteins Deep Learning
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EQUIBIND: A geometric deep learning-based protein-ligand binding prediction method.

Drug discoveries & therapeutics Sep 26, 2023
Structure-based virtual screening plays a critical role in drug discovery. However, numerous docking programs, such as AutoDock Vina and Glide, are time-consuming due to the necessity of generating numerous molecular conformations and executing steps...
Drug Discovery Deep Learning Ligands
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Efficient and accurate large library ligand docking with KarmaDock.

Nature computational science Sep 21, 2023
Ligand docking is one of the core technologies in structure-based virtual screening for drug discovery. However, conventional docking tools and existing deep learning tools may suffer from limited performance in terms of speed, pose quality and bindi...
Ligands Protein Binding Neural Networks, Computer Molecular Docking Simulation Proteins
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