Self-Guided Molecular Simulation Methods.

Authors: Wu X; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA., Brooks BR; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

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

Publication Type: Journal Article; Review

Journal Info: 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

MeSH Terms: 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.

Authors: Balogh G; Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary., Bereczky Z; Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Esther Rubavathy SM; Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India., Rajapandian V; Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India., Prakash M; Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Gao Y; School of Pharmacy and Minhang Hospital, Fudan University, Shanghai 201203, China., Zhu H; School of Pharmacy and Minhang Hospital, Fudan University, Shanghai 201203, China., Gao LX; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China., Xu GY; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China., Lin J; School of Pharmacy and Minhang Hospital, Fudan University, Shanghai 201203, China., Sun L; School of Pharmacy and Minhang Hospital, Fudan University, Shanghai 201203, China., Li W; School of Pharmacy and Minhang Hospital, Fudan University, Shanghai 201203, China., Li J; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. Electronic address: jli@simm.ac.cn., Fu W; School of Pharmacy and Minhang Hospital, Fudan University, Shanghai 201203, China. Electronic address: wfu@fudan.edu.cn.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Locke T; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA., Ferrante A; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA., Li D; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA., Weaver MN; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA., Minkara MS; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA. m.minkara@northeastern.edu.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Zhao C; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China.; The First Clinical Medical College, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Li Y; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China.; The First Clinical Medical College, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Lin J; Academy of Integrative Medicine of Fujian University of Traditional Chinese Medicine, Fuzhou, China.; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Chen Y; College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Zeng J; Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Wang Z; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China.; The First Clinical Medical College, Fujian University of Traditional Chinese Medicine, Fuzhou, China., You Z; The First Clinical Medical College, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Chen Y; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China.; The First Clinical Medical College, Fujian University of Traditional Chinese Medicine, Fuzhou, China., Zhang W; Department of Cardiopulmonary Rehabilitation, Fujian University of Traditional Chinese Medicine Affiliated Rehabilitation Hospital, Fuzhou, China., Huang J; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China., Xie Y; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China., Wu X; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China., Shi R; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China. 13509393654@139.com., Wang J; Department of Anorectal Surgery, The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350004, China. antcity@126.com.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Sridharan Iyer S; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637., Herman KM; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637., Paul T; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637., Wang Y; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637., Pollard TD; Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.; Department of Cell Biology, Yale University, New Haven, CT 06510., Voth GA; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637.

Source: 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.

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Park J; The Interdisciplinary Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Republic of Korea., Lim H; Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea., Lee Y; College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Republic of Korea., Kim T; Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea., Song H; Graduate Program of Industrial Pharmaceutical Science, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea., Lee S; Graduate Program of Industrial Pharmaceutical Science, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea., Heo Y; College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Republic of Korea., Kim J; Department of Integrative Biotechnology, Yonsei University, Incheon 21983, Republic of Korea., Namkung W; College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Republic of Korea., Han G; The Interdisciplinary Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Republic of Korea; Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea; Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; Postech Biotech Center, Pohang, Gyeongbuk 37673, Republic of Korea. Electronic address: gyoonhee@yonsei.ac.kr.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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

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

Authors: Liang J; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China., Zhao Z; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China., Chen X; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China., Tan M; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang, 524088, China., Chen Z; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang, 524088, China., Chen M; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang, 524088, China., Zhang J; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang, 524088, China., Cao W; Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China; College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang, 524088, China. Electronic address: cwenhong@gdou.edu.cn.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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

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

Authors: Gao L; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Jiang X; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Duan H; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Shen Y; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China. shenbmy@126.com., Gu K; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Huang K; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Wang Y; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Shu M; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China., Zhang R; Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, 550002, China., Lin Z; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China. zhlin@cqut.edu.cn.; Chongqing College of Traditional Chinese Medicine, Chongqing, 402760, China. zhlin@cqut.edu.cn.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Chen J; State Key Laboratory of Food Science and Resource, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Food Science Unit, Department of Life Technologies, University of Turku, FI-20014, Finland., Ge W; State Key Laboratory of Food Science and Resource, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China., Wang Y; State Key Laboratory of Food Science and Resource, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China., Hu Z; State Key Laboratory of Food Science and Resource, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China., Lv W; State Key Laboratory of Food Science and Resource, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China., Wang H; State Key Laboratory of Food Science and Resource, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China. Electronic address: hxwang@jiangnan.edu.cn.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Samsonov SA; Faculty of Chemistry, University of Gdańsk, ul, Wita Stwosza 63, 80-308, Gdańsk, Poland. Electronic address: sergey.samsonov@ug.edu.pl., Frączyk T; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland., Ufnalska I; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland., Bal W; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.

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

Publication Type: Journal Article

Journal Info: 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

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

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

Authors: Leon Foun Lin R; Université Paris Cité and Université de la Réunion, INSERM, EFS, BIGR U1134, DSIMB, Bioinformatics team, F-75015, Paris, France., Bellaiche A; Université Paris Cité and Université de la Réunion, INSERM, EFS, BIGR U1134, DSIMB, Bioinformatics team, F-75015, Paris, France., Etchebest C; Université Paris Cité and Université de la Réunion, INSERM, EFS, BIGR U1134, DSIMB, Bioinformatics team, F-75015, Paris, France. Electronic address: catherine.etchebest@inserm.fr.

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

Publication Type: Journal Article; Review

Journal Info: 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

MeSH Terms: 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.

Authors: Khan MTA; Department of Mechanical Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh. Electronic address: tahmidkhan3.1415@gmail.com., Pial TH; The Department of Material Science and Engineering, Johns Hopkins University, Baltimore, MD, United States. Electronic address: mpial1@jh.edu., Motalab M; Department of Mechanical Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh. Electronic address: abdulmotalab@me.buet.ac.bd.

Source: 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.

Publication Type: Journal Article

Journal Info: 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

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

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

Authors: Ait Elmachkouri Y; Laboratory of Organic and physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco. Electronic address: younesse.aitelmachkouri@edu.uiz.ac.ma., Rajesh R; Department of Physics, Vel Tech High Tech Dr.Rangarajan Dr.Sakunthala Engineering College, Avadi, Chennai, Tamil Nadu 600 062, India., Altharawi A; Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia., Frit A AP; Department of Physics, Vel Tech High Tech Dr.Rangarajan Dr.Sakunthala Engineering College, Avadi, Chennai, Tamil Nadu 600 062, India., Alossaimi MA; Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia., Riadi Y; Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia., Aldakhil T; Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia., Taha ML; Laboratory of Organic and physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco., Haggam RA; Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia; Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt. Electronic address: relhaggan@iu.edu.sa.

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

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: 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.

Authors: Zhao L; College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China; Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China. Electronic address: zhaollabc@163.com., Zhao L; Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China. Electronic address: zhaolisdau@163.com., Li H; College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China; Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China. Electronic address: dzxylhy@163.com., Cao Z; Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China. Electronic address: qiayilai@mail.ustc.edu.cn.

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

Publication Type: Journal Article

Journal Info: 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

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

Combining Cryo-EM with Computational Approaches To Revolutionize Structural Biology.

Authors: Kim HU; Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.; Kangwon Center for Systems Imaging, Chuncheon, 24341, Republic of Korea., An MY; Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea., Kim YK; Kangwon Center for Systems Imaging, Chuncheon, 24341, Republic of Korea., Chung JM; Department of Biotechnology, The Catholic University of Korea, Bucheon, 14662, Republic of Korea. jmchung@catholic.ac.kr., Jung HS; Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea. hsjung@kangwon.ac.kr.; Kangwon Center for Systems Imaging, Chuncheon, 24341, Republic of Korea. hsjung@kangwon.ac.kr.

Source: The protein journal [Protein J] 2025 Dec; Vol. 44 (6), pp. 675-690. Date of Electronic Publication: 2025 Oct 16.

Publication Type: Journal Article; Review

Journal Info: Publisher: Springer Country of Publication: Netherlands NLM ID: 101212092 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1875-8355 (Electronic) Linking ISSN: 15723887 NLM ISO Abbreviation: Protein J Subsets: MEDLINE

MeSH Terms: Cryoelectron Microscopy*/methods , Molecular Dynamics Simulation* , Molecular Docking Simulation* , Proteins*/chemistry , Computational Biology*/methods, Protein Conformation ; Humans ; Drug Discovery

Targeting cadherins with colicins: Molecular docking and dynamics reveal disruptive potential in cancer metastasis.

Authors: Vimala PB; Department of Microbiology, SRM Medical College Hospital and Research Center, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India. Electronic address: pb9861@srmist.edu.in., Vajravelu LK; Department of Microbiology, SRM Medical College Hospital and Research Center, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India. Electronic address: leelav@srmist.edu.in., Lathakumari RH; Department of Microbiology, SRM Medical College Hospital and Research Center, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India., Panneerselvam VP; Department of Microbiology, SRM Medical College Hospital and Research Center, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India., Nair DM; Department of Microbiology, SRM Medical College Hospital and Research Center, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India., Thulukkanam J; Department of Microbiology, SRM Medical College Hospital and Research Center, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India.

Source: Computational biology and chemistry [Comput Biol Chem] 2025 Dec; Vol. 119, pp. 108564. Date of Electronic Publication: 2025 Jun 20.

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: Cadherins*/metabolism , Cadherins*/chemistry , Cadherins*/antagonists & inhibitors , Molecular Docking Simulation* , Molecular Dynamics Simulation* , Colicins*/chemistry , Colicins*/metabolism , Colicins*/pharmacology, Humans ; Neoplasm Metastasis ; Protein Binding

The potential mechanism of methamphetamine-induced mitochondrial dysfunction and cell degeneration via direct permeation across mitochondrial membranes: The study on molecular dynamics simulations and in vitro model.

Authors: Polvat T; Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand; Center of Emotional Health, Department of Psychology, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia., Khuntawee W; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand., Prasertporn T; Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand., Promthep K; Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand., Kerdkaen N; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Department of Physics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand., Panmanee J; Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand., Nalakarn P; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Department of Physics, Faculty of Science and Technology, Thammasat University, Pathumthani, 12120, Thailand., Wong-Ekkabut J; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Department of Physics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand. Electronic address: jirasak.w@ku.th., Chetsawang B; Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand. Electronic address: banthit.che@mahidol.ac.th.

Source: Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association [Food Chem Toxicol] 2025 Dec; Vol. 206, pp. 115743. Date of Electronic Publication: 2025 Sep 15.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Science Ltd Country of Publication: England NLM ID: 8207483 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-6351 (Electronic) Linking ISSN: 02786915 NLM ISO Abbreviation: Food Chem Toxicol Subsets: MEDLINE

MeSH Terms: Methamphetamine*/toxicity , Molecular Dynamics Simulation* , Mitochondria*/drug effects , Mitochondria*/metabolism , Mitochondrial Membranes*/drug effects , Mitochondrial Membranes*/metabolism, Dopamine/metabolism ; Dopamine/chemistry ; Humans ; Lipid Bilayers/metabolism ; Lipid Bilayers/chemistry ; Permeability ; Animals ; Apoptosis/drug effects ; Dopamine Plasma Membrane Transport Proteins/metabolism

Molecular dynamics insights into glycosaminoglycan effects on the extracellular domains of syndecan 2 and 4 dimers.

Authors: Samsonov SA; Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308, Gdańsk, Poland. Electronic address: sergey.samsonov@ug.edu.pl., Ricard-Blum S; Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, CNRS, Université Claude Bernard Lyon 1, Univ Lyon, Villeurbanne, 69622, Cedex, France.

Source: Carbohydrate research [Carbohydr Res] 2025 Dec; Vol. 558, pp. 109690. Date of Electronic Publication: 2025 Sep 30.

Publication Type: Journal Article

Journal Info: 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

MeSH Terms: Molecular Dynamics Simulation* , Syndecan-4*/chemistry , Syndecan-4*/metabolism , Glycosaminoglycans*/chemistry , Syndecan-2*/chemistry, Protein Multimerization ; Humans ; Protein Domains ; Animals