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Protein Binding

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Teaching old docks new tricks with machine learning enhanced ensemble docking.

Scientific reports Sep 5, 2024
We here introduce Ensemble Optimizer (EnOpt), a machine-learning tool to improve the accuracy and interpretability of ensemble virtual screening (VS). Ensemble VS is an established method for predicting protein/small-molecule (ligand) binding. Unlike...
Machine Learning Protein Conformation Protein Binding Proteins Software Ligands Molecular Docking Simulation
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An artificial intelligence accelerated virtual screening platform for drug discovery.

Nature communications Sep 5, 2024
Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding p...
Humans Artificial Intelligence Ubiquitin-Protein Ligases Molecular Docking Simulation Small Molecule Libraries Drug Evaluation, Preclinical Drug Discovery NAV1.7 Voltage-Gated Sodium Channel Ligands Protein Binding Crystallography, X-Ray
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Enhancing protein-ligand binding affinity prediction through sequential fusion of graph and convolutional neural networks.

Journal of computational chemistry Sep 2, 2024
Predicting protein-ligand binding affinity is a crucial and challenging task in structure-based drug discovery. With the accumulation of complex structures and binding affinity data, various machine-learning scoring functions, particularly those base...
Protein Binding Proteins Ligands Neural Networks, Computer Drug Discovery Deep Learning
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Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling.

Journal of molecular biology Aug 29, 2024
Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational predictio...
DNA-Binding Proteins Binding Sites Computational Biology DNA Neural Networks, Computer Deep Learning Protein Binding
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From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Aug 29, 2024
Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only ta...
HSP90 Heat-Shock Proteins Drug Design Molecular Dynamics Simulation Deep Learning Ligands Thermodynamics Protein Binding Proteins
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Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning.

Journal of chemical information and modeling Aug 28, 2024
Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and prin...
Mutation Molecular Dynamics Simulation Protein Conformation Deep Learning Normal Distribution Protein Binding Proto-Oncogene Proteins p21(ras) Humans Principal Component Analysis
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Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure.

Journal of chemical information and modeling Aug 28, 2024
We present a computational scheme for predicting the ligands that bind to a pocket of a known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations, and permutati...
Machine Learning Protein Conformation Models, Molecular Binding Sites Algorithms Small Molecule Libraries Molecular Structure Protein Binding Ligands Proteins
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A Point Cloud Graph Neural Network for Protein-Ligand Binding Site Prediction.

International journal of molecular sciences Aug 27, 2024
Predicting protein-ligand binding sites is an integral part of structural biology and drug design. A comprehensive understanding of these binding sites is essential for advancing drug innovation, elucidating mechanisms of biological function, and exp...
Databases, Protein Deep Learning Ligands Protein Binding Binding Sites Proteins Neural Networks, Computer Algorithms
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Chemical analogue based drug design for cancer treatment targeting PI3K: integrating machine learning and molecular modeling.

Molecular diversity Aug 17, 2024
Cancer is a generic term for a group of disorders defined by uncontrolled cell growth and the potential to invade or spread to other parts of the body. Gene and epigenetic alterations disrupt normal cellular control, leading to abnormal cell prolifer...
Phosphatidylinositol 3-Kinases Molecular Dynamics Simulation Ligands Protein Kinase Inhibitors Phosphoinositide-3 Kinase Inhibitors Class Ib Phosphatidylinositol 3-Kinase Antineoplastic Agents Protein Binding Models, Molecular Molecular Docking Simulation Drug Design Humans Machine Learning Neoplasms
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FitScore: a fast machine learning-based score for 3D virtual screening enrichment.

Journal of computer-aided molecular design Aug 16, 2024
Enhancing virtual screening enrichment has become an urgent problem in computational chemistry, driven by increasingly large databases of commercially available compounds, without a commensurate drop in in vitro screening costs. Docking these large d...
Software Molecular Docking Simulation Drug Discovery Humans Machine Learning Ligands Binding Sites Protein Binding Proteins Drug Evaluation, Preclinical
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