AIMC Topic: Models, Molecular

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ActiMut-XGB: Predicting thermodynamic stability of point mutations for CALB with protein language model.

International journal of biological macromolecules Jun 1, 2025
Predicting the functional impact of single-point mutations on protein residual activity, especially after high-temperature incubation, is critical in protein engineering. We present an innovative machine learning model based on eXtreme Gradient Boost...
Models, Molecular Fungal Proteins Machine Learning Protein Engineering Thermodynamics Point Mutation Enzyme Stability Lipase
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Computational methods for modeling protein-protein interactions in the AI era: Current status and future directions.

Drug discovery today Jun 1, 2025
The modeling of protein-protein interactions (PPIs) has been revolutionized by artificial intelligence, with deep learning and end-to-end frameworks such as AlphaFold and its derivatives now dominating the field. This review surveys the current compu...
Protein Interaction Mapping Molecular Docking Simulation Protein Binding Proteins Models, Molecular Computational Biology Humans Artificial Intelligence
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Deciphering the structural complexity of esterases in Amycolatopsis eburnea: A comprehensive exploration of solvent accessibility patterns.

Computers in biology and medicine Jun 1, 2025
Carboxylesterases (CES) are pivotal enzymes in the hydrolysis of carboxylic esters, playing fundamental roles in both biological systems and biotechnological applications. This study investigates CES from the Amycolatopsis genus, characterized by its...
Solvents Bacterial Proteins Machine Learning Actinomycetales Models, Molecular Esterases
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Characterization of conformational flexibility in protein structures by applying artificial intelligence to molecular modeling.

Journal of structural biology Jun 1, 2025
Recent AI applications have revolutionized the modeling of structurally unresolved protein regions, thereby complementing traditional computational methods. These state-of-the-art techniques can generate numerous candidate structures, significantly e...
Ubiquitin Thermodynamics Molecular Dynamics Simulation Protein Conformation Protein Folding Proteins Models, Molecular Artificial Intelligence
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Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks.

Communications biology May 25, 2025
Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when ...
Cryoelectron Microscopy Normal Distribution Models, Molecular Macromolecular Substances Neural Networks, Computer Deep Learning
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EnGCI: enhancing GPCR-compound interaction prediction via large molecular models and KAN network.

BMC biology May 15, 2025
BACKGROUND: Identifying GPCR-compound interactions (GCI) plays a significant role in drug discovery and chemogenomics. Machine learning, particularly deep learning, has become increasingly influential in this domain. Large molecular models, due to th...
Machine Learning Drug Discovery Neural Networks, Computer Receptors, G-Protein-Coupled Deep Learning Models, Molecular
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NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation.

Journal of chemical theory and computation May 13, 2025
Artificial intelligence-based peptide structure prediction methods have revolutionized biomolecular science. However, restricting predictions to peptides composed solely of 20 natural amino acids significantly limits their practical application; as s...
Models, Molecular Amino Acids Peptides, Cyclic Deep Learning Protein Conformation Cyclization
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A deep learning and molecular modeling approach to repurposing Cangrelor as a potential inhibitor of Nipah virus.

Scientific reports May 12, 2025
Deforestation, urbanization, and climate change have significantly increased the risk of zoonotic diseases. Nipah virus (NiV) of Paramyxoviridae family and Henipavirus genus is transmitted by Pteropus bats. Climate-induced changes in bat migration pa...
Drug Repositioning Models, Molecular Alanine Nipah Virus Molecular Dynamics Simulation Deep Learning Antiviral Agents Animals Molecular Docking Simulation Humans RNA-Dependent RNA Polymerase Adenosine Monophosphate Henipavirus Infections
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Machine Learning Classification of Chirality and Optical Rotation Using a Simple One-Hot Encoded Cartesian Coordinate Molecular Representation.

Journal of chemical information and modeling May 12, 2025
Absolute stereochemical configurations and optical rotations were computed for 121,416 molecular structures from the QM9 quantum chemistry data set using density functional theory. A representation for the molecules was developed using Cartesian coor...
Optical Rotation Quantum Theory Stereoisomerism Machine Learning Algorithms Models, Molecular
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Data-Driven Insights into Porphyrin Geometry: Interpretable AI for Non-Planarity and Aromaticity Analyses.

Journal of chemical information and modeling May 12, 2025
Porphyrins are involved in numerous and very different chemical and biological processes, due to the sensitivity of their application-relevant properties to subtle structural changes. Applying modern machine learning methodology is very appealing for...
Machine Learning Porphyrins Structure-Activity Relationship Ligands Models, Molecular
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