AIMC Topic: Protein Binding

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Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA.

Genes Jan 19, 2025
BACKGROUND/OBJECTIVES: Predicting the effects of protein and DNA mutations on the binding free energy of protein-DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions involve pro...
Protein Binding Thermodynamics Mutation Humans DNA Machine Learning DNA-Binding Proteins
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Targeting protein-ligand neosurfaces with a generalizable deep learning tool.

Nature Jan 15, 2025
Molecular recognition events between proteins drive biological processes in living systems. However, higher levels of mechanistic regulation have emerged, in which protein-protein interactions are conditioned to small molecules. Despite recent advanc...
Proteins Models, Molecular Proto-Oncogene Proteins c-bcl-2 Bridged Bicyclo Compounds, Heterocyclic Ligands Drug Design Deep Learning Protein Binding Humans
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Decoding the blueprint of receptor binding by filoviruses through large-scale binding assays and machine learning.

Cell host & microbe Jan 15, 2025
Evidence suggests that bats are important hosts of filoviruses, yet the specific species involved remain largely unidentified. Niemann-Pick C1 (NPC1) is an essential entry receptor, with amino acid variations influencing viral susceptibility and spec...
Filoviridae Infections Protein Binding Animals Receptors, Virus Chiroptera Humans Filoviridae Glycoproteins Phylogeny Hemorrhagic Fever, Ebola Machine Learning Niemann-Pick C1 Protein Ebolavirus
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GraphkmerDTA: integrating local sequence patterns and topological information for drug-target binding affinity prediction and applications in multi-target anti-Alzheimer's drug discovery.

Molecular diversity Jan 10, 2025
Identifying drug-target binding affinity (DTA) plays a critical role in early-stage drug discovery. Despite the availability of various existing methods, there are still two limitations. Firstly, sequence-based methods often extract features from fix...
Alzheimer Disease ErbB Receptors Humans Neural Networks, Computer Deep Learning Drug Discovery Protein Binding
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Integrating machine learning and structural dynamics to explore B-cell lymphoma-2 inhibitors for chronic lymphocytic leukemia therapy.

Molecular diversity Jan 9, 2025
Chronic lymphocytic leukemia (CLL) is a malignancy caused by the overexpression of the anti-apoptotic protein B-cell lymphoma-2 (BCL-2), making it a critical therapeutic target. This study integrates computational screening, molecular docking, and mo...
Humans Machine Learning Leukemia, Lymphocytic, Chronic, B-Cell Protein Binding Molecular Dynamics Simulation Molecular Docking Simulation Proto-Oncogene Proteins c-bcl-2 Antineoplastic Agents
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Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models.

Journal of chemical information and modeling Jan 9, 2025
The accurate identification of protein-nucleotide binding residues is crucial for protein function annotation and drug discovery. Numerous computational methods have been proposed to predict these binding residues, achieving remarkable performance. H...
Binding Sites Proteins Databases, Protein Nucleotides Deep Learning Protein Binding
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Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein-Protein Interactions.

Journal of chemical information and modeling Jan 7, 2025
Predicting protein-protein interaction (PPI) binding affinities in unseen protein complex clusters is essential for elucidating complex protein interactions and for the targeted screening of peptide- or protein-based drugs. We introduce MCGLPPI++, a ...
Protein Interaction Mapping Machine Learning Protein Binding Proteins Receptors, Antigen, T-Cell
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Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables.

Journal of chemical information and modeling Jan 7, 2025
Enhanced sampling (ES) simulations of biomolecular recognition, such as binding small molecules to proteins and nucleic acid targets, protein-protein association, and protein-nucleic acid interactions, have gained significant attention in the simulat...
RNA, Viral Molecular Dynamics Simulation Nucleic Acid Conformation RNA Deep Learning Protein Binding Peptides
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Data and AI-driven synthetic binding protein discovery.

Trends in pharmacological sciences Jan 3, 2025
Synthetic binding proteins (SBPs) are a class of protein binders that are artificially created and do not exist naturally. Their broad applications in tackling challenges of research, diagnostics, and therapeutics have garnered significant interest. ...
Drug Discovery Protein Binding Computational Biology Artificial Intelligence Animals Protein Engineering Proteins Models, Molecular Humans
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Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein-Ligand Binding Free Energies.

Journal of chemical theory and computation Jan 3, 2025
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several ti...
Machine Learning Protein Binding Quantum Theory Proteins Ligands Molecular Dynamics Simulation Thermodynamics
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