Výsledky vyhledávání - "MOLECULAR dynamics"

Self-Guided Molecular Simulation Methods.

Autoři: Wu X Brooks BR

Zdroj: International journal of molecular sciences [Int J Mol Sci] 2025 Oct 26; Vol. 26 (21). Date of Electronic Publication: 2025 Oct 26.

Způsob vydávání: Journal Article; Review

Informace o časopise: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation*, Algorithms

The Effects of Heparin Binding and Arg596 Mutations on the Conformation of Thrombin-Antithrombin Michaelis Complex, Revealed by Enhanced Sampling Molecular Dynamics Simulations.

Autoři: Balogh G Bereczky Z

Zdroj: International journal of molecular sciences [Int J Mol Sci] 2025 Oct 11; Vol. 26 (20). Date of Electronic Publication: 2025 Oct 11.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Thrombin*/chemistry , Thrombin*/genetics , Thrombin*/metabolism , Heparin*/metabolism , Heparin*/chemistry , Mutation* , Antithrombins*/chemistry , Antithrombins*/metabolism , Arginine*/genetics , Arginine*/chemistry, Protein Binding ; Humans ; Molecular Docking Simulation ; Protein Conformation ; Binding Sites ; Prothrombin/genetics ; Prothrombin/chemistry ; Prothrombin/metabolism

Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics.

Autoři: Esther Rubavathy SM Rajapandian V Prakash M

Zdroj: Journal of biomolecular structure & dynamics [J Biomol Struct Dyn] 2025 Oct; Vol. 43 (16), pp. 8984-8995. Date of Electronic Publication: 2024 Mar 08.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Taylor & Francis Country of Publication: England NLM ID: 8404176 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1538-0254 (Electronic) Linking ISSN: 07391102 NLM ISO Abbreviation: J Biomol Struct Dyn Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Histone Deacetylase Inhibitors*/chemistry , Histone Deacetylase Inhibitors*/pharmacology , Histone Deacetylases*/chemistry , Histone Deacetylases*/metabolism , Hydroxamic Acids*/chemistry , Hydroxamic Acids*/pharmacology , Zinc*/chemistry , Zinc*/metabolism , Histone Deacetylase 1*/antagonists & inhibitors , Histone Deacetylase 1*/chemistry, Molecular Docking Simulation ; Protein Binding ; Humans ; Binding Sites ; Ligands

Structure-based design of novel THR-β agonists and mechanism of activation research by molecular dynamics simulations.

Autoři: Gao Y Zhu H Gao LX a další

Zdroj: Bioorganic & medicinal chemistry [Bioorg Med Chem] 2025 Dec 15; Vol. 131, pp. 118397. Date of Electronic Publication: 2025 Sep 22.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Science Country of Publication: England NLM ID: 9413298 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1464-3391 (Electronic) Linking ISSN: 09680896 NLM ISO Abbreviation: Bioorg Med Chem Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Drug Design* , Thyroid Hormone Receptors beta*/agonists , Thyroid Hormone Receptors beta*/metabolism, Humans ; Structure-Activity Relationship ; Molecular Structure ; Ligands

Conformational changes of surfactant protein B due to the alveolar air/liquid interface using molecular dynamics.

Autoři: Locke T Ferrante A Li D a další

Zdroj: Journal of molecular modeling [J Mol Model] 2025 Dec 04; Vol. 32 (1), pp. 4. Date of Electronic Publication: 2025 Dec 04.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Springer Country of Publication: Germany NLM ID: 9806569 Publication Model: Electronic Cited Medium: Internet ISSN: 0948-5023 (Electronic) Linking ISSN: 09485023 NLM ISO Abbreviation: J Mol Model Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Pulmonary Surfactant-Associated Protein B*/chemistry , Pulmonary Alveoli*/chemistry , Pulmonary Alveoli*/metabolism, Hydrophobic and Hydrophilic Interactions ; Protein Conformation ; Water/chemistry ; Solvents/chemistry

Mechanisms of Okanin against wound healing based on network pharmacology, molecular docking and molecular dynamics simulation.

Autoři: Zhao C Li Y Lin J a další

Zdroj: Scientific reports [Sci Rep] 2025 Dec 02; Vol. 15 (1), pp. 43034. Date of Electronic Publication: 2025 Dec 02.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Docking Simulation* , Molecular Dynamics Simulation* , Wound Healing*/drug effects , Network Pharmacology* , Flavonoids*/pharmacology , Flavonoids*/chemistry, Animals ; Mice ; Humans ; Male ; Protein Interaction Maps/drug effects

Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example.

Autoři: Sridharan Iyer S Herman KM Paul T a další

Zdroj: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2025 Dec 02; Vol. 122 (48), pp. e2521421122. Date of Electronic Publication: 2025 Nov 25.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE

Výrazy ze slovníku MeSH: Cryoelectron Microscopy*/methods , Molecular Dynamics Simulation* , Actin Cytoskeleton*/chemistry , Actin Cytoskeleton*/ultrastructure , Actin Cytoskeleton*/metabolism, Adenosine Triphosphate/metabolism ; Adenosine Triphosphate/chemistry ; Adenosine Diphosphate/chemistry ; Adenosine Diphosphate/metabolism ; Actins/chemistry ; Temperature ; Protein Conformation

Discovery of PAR2 antagonists through fragment molecular orbital-based hotspot analysis and allosteric sodium site dynamics simulations.

Autoři: Park J Lim H Lee Y a další

Zdroj: Bioorganic chemistry [Bioorg Chem] 2025 Dec; Vol. 167, pp. 109285. Date of Electronic Publication: 2025 Nov 21.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Country of Publication: United States NLM ID: 1303703 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1090-2120 (Electronic) Linking ISSN: 00452068 NLM ISO Abbreviation: Bioorg Chem Subsets: MEDLINE

Výrazy ze slovníku MeSH: Receptor, PAR-2*/antagonists & inhibitors , Receptor, PAR-2*/metabolism , Molecular Dynamics Simulation* , Drug Discovery* , Sodium*/metabolism , Sodium*/chemistry, Humans ; Allosteric Site/drug effects ; Molecular Structure ; Structure-Activity Relationship ; Dose-Response Relationship, Drug ; Molecular Docking Simulation

Encapsulation of curcumin in groundnut oil-in-water (O/W) nanoemulsions: Experimental analysis and molecular dynamics simulations.

Autoři: Mathias GN Krishna Goud KV Divi S a další

Zdroj: Ultrasonics sonochemistry [Ultrason Sonochem] 2025 Dec; Vol. 123, pp. 107686. Date of Electronic Publication: 2025 Nov 23.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Science Country of Publication: Netherlands NLM ID: 9433356 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-2828 (Electronic) Linking ISSN: 13504177 NLM ISO Abbreviation: Ultrason Sonochem Subsets: MEDLINE

Výrazy ze slovníku MeSH: Curcumin*/chemistry , Molecular Dynamics Simulation* , Water*/chemistry , Plant Oils*/chemistry , Nanostructures*/chemistry, Emulsions/chemistry ; Polysorbates/chemistry ; Drug Compounding ; Antioxidants/chemistry ; Particle Size

Unraveling the molecular interaction mechanisms of antifreeze peptides with ice crystals and myofibrillar proteins: Insights from multispectral and molecular simulation analyses.

Autoři: Liang J Zhao Z Chen X a další

Zdroj: International journal of biological macromolecules [Int J Biol Macromol] 2025 Dec; Vol. 333 (Pt 2), pp. 148881. Date of Electronic Publication: 2025 Nov 07.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 7909578 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0003 (Electronic) Linking ISSN: 01418130 NLM ISO Abbreviation: Int J Biol Macromol Subsets: MEDLINE

Výrazy ze slovníku MeSH: Antifreeze Proteins*/chemistry , Antifreeze Proteins*/metabolism , Ice* , Molecular Dynamics Simulation* , Muscle Proteins*/chemistry , Muscle Proteins*/metabolism , Peptides*/chemistry , Myofibrils*/chemistry , Myofibrils*/metabolism, Protein Binding ; Animals ; Crystallization

Discovery of Potential GPRC5D Inhibitors through Virtual Screening and Molecular Dynamics Simulations.

Autoři: Chen X Yang X Chen R a další

Zdroj: ChemistryOpen [ChemistryOpen] 2025 Dec; Vol. 14 (12), pp. e202500360. Date of Electronic Publication: 2025 Sep 07.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Wiley-VCH Verlag Country of Publication: Germany NLM ID: 101594811 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2191-1363 (Electronic) Linking ISSN: 21911363 NLM ISO Abbreviation: ChemistryOpen Subsets: MEDLINE

Výrazy ze slovníku MeSH: Receptors, G-Protein-Coupled*/antagonists & inhibitors , Receptors, G-Protein-Coupled*/metabolism , Molecular Dynamics Simulation* , Drug Discovery* , Small Molecule Libraries*/chemistry , Small Molecule Libraries*/pharmacology, Humans ; Ligands ; Drug Evaluation, Preclinical

Molecular dynamics simulation-driven focused virtual screening and experimental validation of Fisetin as an inhibitor of Helicobacter pylori HtrA protease.

Autoři: Gao L Jiang X Duan H a další

Zdroj: Molecular diversity [Mol Divers] 2025 Dec; Vol. 29 (6), pp. 6243-6258. Date of Electronic Publication: 2025 Feb 23.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: ESCOM Science Publishers Country of Publication: Netherlands NLM ID: 9516534 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-501X (Electronic) Linking ISSN: 13811991 NLM ISO Abbreviation: Mol Divers Subsets: MEDLINE

Výrazy ze slovníku MeSH: Helicobacter pylori*/enzymology , Helicobacter pylori*/drug effects , Molecular Dynamics Simulation* , Anti-Bacterial Agents*/pharmacology , Anti-Bacterial Agents*/chemistry , Flavonoids*/pharmacology , Flavonoids*/chemistry , Bacterial Proteins*/antagonists & inhibitors , Bacterial Proteins*/chemistry , Bacterial Proteins*/metabolism , Serine Proteinase Inhibitors*/pharmacology , Serine Proteinase Inhibitors*/chemistry , High-Temperature Requirement A Serine Peptidase 1*/antagonists & inhibitors , High-Temperature Requirement A Serine Peptidase 1*/chemistry, Flavonols ; Molecular Docking Simulation ; Humans ; Caseins/metabolism ; Drug Evaluation, Preclinical

Identification and characterization of chia seed peptides with ADH/ALDH activation activity: Insights from molecular docking and molecular dynamics simulation.

Autoři: Chen J Ge W Wang Y a další

Zdroj: Food research international (Ottawa, Ont.) [Food Res Int] 2025 Dec; Vol. 221 (Pt 2), pp. 117324. Date of Electronic Publication: 2025 Aug 13.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Published on behalf of the Canadian Institute of Food Science and Technology by Elsevier Applied Science Country of Publication: Canada NLM ID: 9210143 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-7145 (Electronic) Linking ISSN: 09639969 NLM ISO Abbreviation: Food Res Int Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Docking Simulation* , Seeds*/chemistry , Molecular Dynamics Simulation* , Alcohol Dehydrogenase*/metabolism , Alcohol Dehydrogenase*/chemistry , Salvia*/chemistry , Salvia*/enzymology , Aldehyde Dehydrogenase*/metabolism , Aldehyde Dehydrogenase*/chemistry , Peptides*/chemistry , Peptides*/metabolism, Molecular Weight ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Salvia hispanica ; Plant Extracts

Molecular dynamics study of the impact of glycosylation on conformational properties of trimeric N-terminal domain of human copper transporter 1.

Autoři: Samsonov SA Frączyk T Ufnalska I a další

Zdroj: Carbohydrate research [Carbohydr Res] 2025 Dec; Vol. 558, pp. 109708. Date of Electronic Publication: 2025 Oct 18.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 0043535 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-426X (Electronic) Linking ISSN: 00086215 NLM ISO Abbreviation: Carbohydr Res Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Copper Transporter 1*/chemistry , Cation Transport Proteins*/chemistry , Cation Transport Proteins*/metabolism, Glycosylation ; Humans ; Protein Domains ; Copper/metabolism ; Protein Conformation

Drug Repurposing Investigation for Combating Ebola Virus Disease: Database Mining, Docking Calculations, Molecular Dynamics, and Density Functional Theory Study.

Autoři: Abdelrahman AHM Mekhemer GAH Sidhom PA a další

Zdroj: ChemistryOpen [ChemistryOpen] 2025 Dec; Vol. 14 (12), pp. e202500348. Date of Electronic Publication: 2025 Sep 02.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Wiley-VCH Verlag Country of Publication: Germany NLM ID: 101594811 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2191-1363 (Electronic) Linking ISSN: 21911363 NLM ISO Abbreviation: ChemistryOpen Subsets: MEDLINE

Výrazy ze slovníku MeSH: Drug Repositioning* , Molecular Dynamics Simulation* , Antiviral Agents*/chemistry , Antiviral Agents*/pharmacology , Ebolavirus*/drug effects , Hemorrhagic Fever, Ebola*/drug therapy , Density Functional Theory* , Viral Regulatory and Accessory Proteins*/antagonists & inhibitors , Viral Regulatory and Accessory Proteins*/metabolism, Molecular Docking Simulation ; Humans ; Data Mining

The key role of the dynamics and flexibility of proteins in functional mechanisms: How computational methods can contribute to their identification.

Autoři: Leon Foun Lin R Bellaiche A Etchebest C

Zdroj: Biochimie [Biochimie] 2025 Dec; Vol. 239 (Pt B), pp. 8-26. Date of Electronic Publication: 2025 Oct 14.

Způsob vydávání: Journal Article; Review

Informace o časopise: Publisher: Editions Scientifiques Elsevier Country of Publication: France NLM ID: 1264604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1638-6183 (Electronic) Linking ISSN: 03009084 NLM ISO Abbreviation: Biochimie Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Proteins*/chemistry , Proteins*/metabolism , Computational Biology*/methods, Protein Conformation ; Humans

Electric field-induced modulation of mechanical behavior in polyelectrolyte materials: A multiscale molecular dynamics study.

Autoři: Khan MTA Pial TH Motalab M

Zdroj: Journal of the mechanical behavior of biomedical materials [J Mech Behav Biomed Mater] 2025 Dec; Vol. 172, pp. 107179. Date of Electronic Publication: 2025 Aug 29.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101322406 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-0180 (Electronic) Linking ISSN: 18780180 NLM ISO Abbreviation: J Mech Behav Biomed Mater Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Mechanical Phenomena* , Electricity* , Polymers*/chemistry , Electrolytes*/chemistry, Polystyrenes/chemistry ; Stress, Mechanical

Deciphering the Therapeutic Mechanisms of Wuzi Yanzong Pill for Asthenozoospermia: A Synergistic Approach Combining Bioinformatics and Molecular Dynamics.

Autoři: Liu ZH Li SY Li BJ a další

Zdroj: Cell biochemistry and biophysics [Cell Biochem Biophys] 2025 Dec; Vol. 83 (4), pp. 5181-5196. Date of Electronic Publication: 2025 Aug 09.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Humana Press Country of Publication: United States NLM ID: 9701934 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1559-0283 (Electronic) Linking ISSN: 10859195 NLM ISO Abbreviation: Cell Biochem Biophys Subsets: MEDLINE

Výrazy ze slovníku MeSH: Drugs, Chinese Herbal*/therapeutic use , Drugs, Chinese Herbal*/pharmacology , Drugs, Chinese Herbal*/chemistry , Asthenozoospermia*/drug therapy , Asthenozoospermia*/metabolism , Asthenozoospermia*/genetics , Computational Biology* , Molecular Dynamics Simulation*, Male ; Humans ; Molecular Docking Simulation ; Protein Interaction Maps/drug effects ; Signal Transduction/drug effects ; Network Pharmacology ; Gene Ontology ; Steroid 17-alpha-Hydroxylase/metabolism ; Steroid 17-alpha-Hydroxylase/chemistry

Synthesis, molecular structure, spectroscopic, electronic properties, molecular docking, and molecular dynamics studies on novel 1,2,3-triazole-thiosemicarbazone: A potent breast cancer drug.

Autoři: Ait Elmachkouri Y Rajesh R Altharawi A a další

Zdroj: Computational biology and chemistry [Comput Biol Chem] 2025 Dec; Vol. 119, pp. 108580. Date of Electronic Publication: 2025 Jul 02.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Country of Publication: England NLM ID: 101157394 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-928X (Electronic) Linking ISSN: 14769271 NLM ISO Abbreviation: Comput Biol Chem Subsets: MEDLINE

Výrazy ze slovníku MeSH: Triazoles*/chemistry , Triazoles*/pharmacology , Triazoles*/chemical synthesis , Thiosemicarbazones*/chemistry , Thiosemicarbazones*/pharmacology , Thiosemicarbazones*/chemical synthesis , Molecular Dynamics Simulation* , Molecular Docking Simulation* , Antineoplastic Agents*/chemical synthesis , Antineoplastic Agents*/chemistry , Antineoplastic Agents*/pharmacology , Breast Neoplasms*/drug therapy , Breast Neoplasms*/metabolism, Molecular Structure ; Humans ; Density Functional Theory ; Female ; Electrons

Effects of toxin peptides PepA1 and PepA2 on human red blood cell membrane model: A molecular dynamics study.

Autoři: Zhao L Li H Cao Z

Zdroj: Computational biology and chemistry [Comput Biol Chem] 2025 Dec; Vol. 119, pp. 108552. Date of Electronic Publication: 2025 Jun 14.

Způsob vydávání: Journal Article

Informace o časopise: Publisher: Elsevier Country of Publication: England NLM ID: 101157394 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-928X (Electronic) Linking ISSN: 14769271 NLM ISO Abbreviation: Comput Biol Chem Subsets: MEDLINE

Výrazy ze slovníku MeSH: Molecular Dynamics Simulation* , Erythrocyte Membrane*/drug effects , Peptides*/chemistry , Peptides*/pharmacology, Humans ; Amino Acid Sequence