AIMC Topic: Binding Sites

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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...
Machine Learning Software Molecular Docking Simulation Humans Drug Evaluation, Preclinical Ligands Binding Sites Drug Discovery Protein Binding Proteins
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MultiModRLBP: A Deep Learning Approach for Multi-Modal RNA-Small Molecule Ligand Binding Sites Prediction.

IEEE journal of biomedical and health informatics Aug 6, 2024
This study aims to tackle the intricate challenge of predicting RNA-small molecule binding sites to explore the potential value in the field of RNA drug targets. To address this challenge, we propose the MultiModRLBP method, which integrates multi-mo...
Algorithms Deep Learning Nucleic Acid Conformation Binding Sites Small Molecule Libraries Computational Biology RNA Ligands
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Protein ligand binding site prediction using graph transformer neural network.

PloS one Aug 6, 2024
Ligand binding site prediction is a crucial initial step in structure-based drug discovery. Although several methods have been proposed previously, including those using geometry based and machine learning techniques, their accuracy is considered to ...
Drug Discovery Databases, Protein Neural Networks, Computer Protein Binding Machine Learning Ligands Algorithms Proteins Binding Sites
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Geometric deep learning of protein-DNA binding specificity.

Nature methods Aug 5, 2024
Predicting protein-DNA binding specificity is a challenging yet essential task for understanding gene regulation. Protein-DNA complexes usually exhibit binding to a selected DNA target site, whereas a protein binds, with varying degrees of binding sp...
Deep Learning Binding Sites Protein Binding Computational Biology DNA Models, Molecular DNA-Binding Proteins
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Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning.

Food chemistry Aug 3, 2024
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins thr...
Quantitative Structure-Activity Relationship Binding Sites Xanthine Oxidase Molecular Docking Simulation Machine Learning Swine Animals Enzyme Inhibitors Peptides
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Combined structure-based virtual screening and machine learning approach for the identification of potential dual inhibitors of ACC and DGAT2.

International journal of biological macromolecules Jul 31, 2024
Acetyl-coenzyme A carboxylase (ACC) and diacylglycerol acyltransferase 2 (DGAT2) are recognized as potential therapeutic targets for nonalcoholic fatty liver disease (NAFLD). Inhibitors targeting ACC and DGAT2 have exhibited the capacity to reduce he...
Non-alcoholic Fatty Liver Disease Enzyme Inhibitors Binding Sites Protein Binding Humans Molecular Dynamics Simulation Diacylglycerol O-Acyltransferase Drug Evaluation, Preclinical Machine Learning Acetyl-CoA Carboxylase Molecular Docking Simulation
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pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.

Life science alliance Jul 30, 2024
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologie...
Binding Sites Machine Learning Proteome Databases, Protein Software Computational Biology Humans RNA Protein Binding RNA-Binding Proteins Proteomics
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Cross-Species Prediction of Transcription Factor Binding by Adversarial Training of a Novel Nucleotide-Level Deep Neural Network.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Jul 30, 2024
Cross-species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross-species predictive performance being consistently worse than within-species performance. In thi...
Humans Neural Networks, Computer Animals Deep Learning Mice Nucleotides Species Specificity Polymorphism, Single Nucleotide Binding Sites Computational Biology Transcription Factors
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Binding and sensing diverse small molecules using shape-complementary pseudocycles.

Science (New York, N.Y.) Jul 18, 2024
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying sha...
Protein Multimerization Nanopores Proteins Thyroxine Methotrexate Ligands Binding Sites Small Molecule Libraries Molecular Docking Simulation Deep Learning Protein Binding
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Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning.

Molecules (Basel, Switzerland) Jul 18, 2024
Inhibiting MDM2-p53 interaction is considered an efficient mode of cancer treatment. In our current study, Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and binding free energy calculations were combined together to probe the bi...
Protein Structure, Secondary Proto-Oncogene Proteins c-mdm2 Protein Structure, Tertiary Peptides Deep Learning Molecular Dynamics Simulation Protein Binding Hydrogen Bonding Binding Sites
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