AIMC Topic: Molecular Dynamics Simulation

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Deep learning-driven semi-rational design in phenylalanine ammonia-lyase for enhanced catalytic efficiency.

International journal of biological macromolecules Feb 19, 2025
Phenylalanine ammonia-lyase (PAL) possesses significant potential in agriculture, industry, and the treatment of various diseases, including cancer. In particular, PAL derived from Anabaena variabilis (AvPAL) has been successfully utilized in clinica...
Mutation Kinetics Molecular Dynamics Simulation Biocatalysis Deep Learning Phenylalanine Ammonia-Lyase Protein Engineering Catalysis Anabaena variabilis
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Identification of potent phytochemicals against Magnaporthe oryzae through machine learning aided-virtual screening and molecular dynamics simulation approach.

Computers in biology and medicine Feb 17, 2025
Magnaporthe oryzae stands as a notorious fungal pathogen responsible for causing devastating blast disease in cereals, leading to substantial reductions in grain production. Despite the usage of chemical fungicides to combat the pathogen, their effec...
Fungal Proteins Ascomycota Magnaporthe Fungicides, Industrial Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Phytochemicals Plant Diseases
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Accurate Prediction of ωB97X-D/6-31G* Equilibrium Geometries from a Neural Net Starting from Merck Molecular Force Field (MMFF) Molecular Mechanics Geometries.

Journal of chemical information and modeling Feb 17, 2025
Starting from Merck Molecular Force Field (MMFF) geometries, a neural-net based model has been formulated to closely reproduce ωB97X-D/6-31G* equilibrium geometries for organic molecules. The model involves training to >6 million energy and force cal...
Neural Networks, Computer Biological Products Molecular Dynamics Simulation Molecular Conformation
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Machine learning and cheminformatics-based Identification of lichen-derived compounds targeting mutant PBP4 in Staphylococcus aureus.

Molecular diversity Feb 15, 2025
Penicillin-binding protein 4 (PBP4) is essential in imparting significant β-lactam antibiotics resistance in Staphylococcus aureus (S. aureus) and the mutation R200L in PBP4 is linked to β-lactam non-susceptibility in natural strains, complicating tr...
Mutation Molecular Dynamics Simulation Cheminformatics Molecular Docking Simulation Machine Learning Staphylococcus aureus Lichens Penicillin-Binding Proteins Anti-Bacterial Agents Bacterial Proteins
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A semiempirical and machine learning approach for fragment-based structural analysis of non-hydroxamate HDAC3 inhibitors.

Biophysical chemistry Feb 15, 2025
Interest in HDAC3 inhibitors (HDAC3i) for pharmacological applications outside of cancer is growing. However, concerns regarding the possible mutagenicity of the commonly used hydroxamates (zinc-binding groups, ZBGs) are also increasing. Considering ...
Molecular Structure Humans Molecular Dynamics Simulation Histone Deacetylase Inhibitors Machine Learning Quantum Theory Quantitative Structure-Activity Relationship Molecular Docking Simulation Histone Deacetylases Thermodynamics
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Artificial Intuition and accelerating the process of antimicrobial drug discovery.

Computers in biology and medicine Feb 14, 2025
New drug development is a very challenging, expensive, and usually time-consuming process. This issue is very important with regard to antimicrobials, which are affected by the global issue of the development and spread of resistance. This framework ...
Drug Discovery Computational Biology Humans Artificial Intelligence Molecular Dynamics Simulation Antitubercular Agents Anti-Infective Agents Mycobacterium tuberculosis
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Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning.

Journal of chemical information and modeling Feb 14, 2025
Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex mol...
Protein Conformation Protein Multimerization Density Functional Theory Molecular Dynamics Simulation Electrons Machine Learning Peptides
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Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.

Journal of molecular biology Feb 12, 2025
Motivated by recent deep mutational scanning (DMS) experiments, we have carried out a diverse set of computations to better understand the distribution and contributions of allostery hotspot residues in a transcription factor, TetR. These include ext...
Computational Biology Thermodynamics Proteins Allosteric Site Models, Molecular Molecular Dynamics Simulation Machine Learning Allosteric Regulation Protein Conformation Protein Binding Mutation
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AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction.

Journal of chemical information and modeling Feb 11, 2025
Accurate prediction of molecular geometries is crucial for drug discovery and materials science. Existing fast conformer prediction algorithms often rely on approximate empirical energy functions, resulting in low accuracy. More accurate methods like...
Molecular Conformation Molecular Dynamics Simulation Diffusion Algorithms Drug Discovery Machine Learning
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Modeling Boltzmann-weighted structural ensembles of proteins using artificial intelligence-based methods.

Current opinion in structural biology Feb 8, 2025
This review highlights recent advances in AI-driven methods for generating Boltzmann-weighted structural ensembles, which are crucial for understanding biomolecular dynamics and drug discovery. With the rise of deep learning models such as AlphaFold2...
Artificial Intelligence Drug Discovery Models, Molecular Molecular Dynamics Simulation Protein Conformation Deep Learning Proteins
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