 Molecular Dynamics Simulation
"Molecular Dynamics Simulation" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus,
MeSH (Medical Subject Headings). Descriptors are arranged in a hierarchical structure,
which enables searching at various levels of specificity.
A computer simulation developed to study the motion of molecules over a period of time.
| Descriptor ID |
D056004
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| MeSH Number(s) |
E05.599.595.500 G02.575.750 L01.224.160.500
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| Concept/Terms |
Molecular Dynamics Simulation- Molecular Dynamics Simulation
- Dynamics Simulation, Molecular
- Dynamics Simulations, Molecular
- Simulation, Molecular Dynamics
- Simulations, Molecular Dynamics
- Molecular Dynamics Simulations
Molecular Dynamics- Molecular Dynamics
- Dynamic, Molecular
- Dynamics, Molecular
- Molecular Dynamic
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Below are MeSH descriptors whose meaning is more general than "Molecular Dynamics Simulation".
Below are MeSH descriptors whose meaning is more specific than "Molecular Dynamics Simulation".
This graph shows the total number of publications written about "Molecular Dynamics Simulation" by people in UAMS Profiles by year, and whether "Molecular Dynamics Simulation" was a major or minor topic of these publications.
To see the data from this visualization as text, click here.
| Year | Major Topic | Minor Topic | Total |
|---|
| 2025 | 0 | 1 | 1 | | 2024 | 1 | 1 | 2 | | 2023 | 0 | 1 | 1 | | 2022 | 0 | 1 | 1 | | 2021 | 0 | 2 | 2 | | 2020 | 2 | 2 | 4 | | 2019 | 2 | 4 | 6 | | 2018 | 0 | 2 | 2 | | 2017 | 0 | 2 | 2 | | 2016 | 0 | 1 | 1 | | 2015 | 1 | 0 | 1 | | 2014 | 1 | 1 | 2 | | 2013 | 0 | 3 | 3 | | 2012 | 1 | 0 | 1 | | 2011 | 1 | 1 | 2 |
To return to the timeline, click here.
Below are the most recent publications written about "Molecular Dynamics Simulation" by people in Profiles over the past ten years.
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Saif A, Islam MT, Raihan MO, Yousefi N, Rahman MA, Faridi H, Hasan AR, Hossain MM, Saleem RM, Albadrani GM, Al-Ghadi MQ, Ahasan Setu MA, Kamel M, Abdel-Daim MM, Aktaruzzaman M. Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches. Comput Biol Med. 2025 May; 190:110044.
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Khalil MI, Helal M, El-Sayed AF, El Hajj R, Holail J, Houssein M, Waraky A, Pardo OE. S6K2 in Focus: Signaling Pathways, Post-Translational Modifications, and Computational Analysis. Int J Mol Sci. 2024 Dec 28; 26(1).
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proc Natl Acad Sci U S A. 2024 Sep 03; 121(36):e2318527121.
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Anishkin A, Adepu KK, Bhandari D, Adams SH, Chintapalli SV. Computational Analysis Reveals Unique Binding Patterns of Oxygenated and Deoxygenated Myoglobin to the Outer Mitochondrial Membrane. Biomolecules. 2023 07 17; 13(7).
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Adepu KK, Kachhap S, Bhandari D, Anishkin A, Chintapalli SV. Computational insights on molecular interactions of acifran with GPR109A and GPR109B. J Mol Model. 2022 Jul 28; 28(8):237.
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Shady NH, Hayallah AM, Mohamed MFA, Ghoneim MM, Chilingaryan G, Al-Sanea MM, Fouad MA, Kamel MS, Abdelmohsen UR. Targeting 3CLpro and SARS-CoV-2 RdRp by Amphimedon sp. Metabolites: A Computational Study. Molecules. 2021 Jun 21; 26(12).
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Jin X, Fu Q, Gu Z, Zhang Z, Lv H. Chitosan/PDLLA-PEG-PDLLA solution preparation by simple stirring and formation into a hydrogel at body temperature for whole wound healing. Int J Biol Macromol. 2021 Aug 01; 184:787-796.
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Albohy A, Zahran EM, Abdelmohsen UR, Salem MA, Al-Warhi T, Al-Sanea MM, Abelyan N, Khalil HE, Desoukey SY, Fouad MA, Kamel MS. Multitarget in silico studies of Ocimum menthiifolium, family Lamiaceae against SARS-CoV-2 supported by molecular dynamics simulation. J Biomol Struct Dyn. 2022 06; 40(9):4062-4072.
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Schnetler R, Fanucchi S, Moldoveanu T, Koorsen G. Linker Histone H1.2 Directly Activates BAK through the K/RVVKP Motif on the C-Terminal Domain. Biochemistry. 2020 09 15; 59(36):3332-3346.
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Drew ED, Janes RW. PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures. Nucleic Acids Res. 2020 07 02; 48(W1):W17-W24.
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Balasubramaniam M, Lakkaniga NR, Dera AA, Fayi MA, Abohashrh M, Ahmad I, Chandramoorthy HC, Nalini G, Rajagopalan P. FCX-146, a potent allosteric inhibitor of Akt kinase in cancer cells: Lead optimization of the second-generation arylidene indanone scaffold. Biotechnol Appl Biochem. 2021 Feb; 68(1):82-91.
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Lakkaniga NR, Balasubramaniam M, Zhang S, Frett B, Li HY. Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics. AAPS J. 2019 12 18; 22(1):14.
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Li X, Dai J, Ni D, He X, Zhang H, Zhang J, Fu Q, Liu Y, Lu S. Insight into the mechanism of allosteric activation of PI3Ka by oncoprotein K-Ras4B. Int J Biol Macromol. 2020 Feb 01; 144:643-655.
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Juvvadi PR, Fox D, Bobay BG, Hoy MJ, Gobeil SMC, Venters RA, Chang Z, Lin JJ, Averette AF, Cole DC, Barrington BC, Wheaton JD, Ciofani M, Trzoss M, Li X, Lee SC, Chen YL, Mutz M, Spicer LD, Schumacher MA, Heitman J, Steinbach WJ. Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents. Nat Commun. 2019 09 19; 10(1):4275.
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Li J, Wu G, Fu Q, Ge H, Liu S, Li X, Cheng B. Exploring the influence of conserved lysine69 on the catalytic activity of the helicobacter pylori shikimate dehydrogenase: A combined QM/MM and MD simulations. Comput Biol Chem. 2019 Dec; 83:107098.
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Zahran EM, Abdelmohsen UR, Hussein AS, Salem MA, Khalil HE, Yehia Desoukey S, Fouad MA, Kamel MS. Antiulcer potential and molecular docking of flavonoids from Ocimum forskolei Benth., family Lamiaceae. Nat Prod Res. 2021 Jun; 35(11):1933-1937.
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Lee T, Christov PP, Shaw S, Tarr JC, Zhao B, Veerasamy N, Jeon KO, Mills JJ, Bian Z, Sensintaffar JL, Arnold AL, Fogarty SA, Perry E, Ramsey HE, Cook RS, Hollingshead M, Davis Millin M, Lee KM, Koss B, Budhraja A, Opferman JT, Kim K, Arteaga CL, Moore WJ, Olejniczak ET, Savona MR, Fesik SW. Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors That Demonstrate in Vivo Activity in Mouse Xenograft Models of Human Cancer. J Med Chem. 2019 04 25; 62(8):3971-3988.
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Chintapalli SV, Anishkin A, Adams SH. Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin. Arch Biochem Biophys. 2018 10 01; 655:56-66.
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Hong WC, Wasko MJ, Wilkinson DS, Hiranita T, Li L, Hayashi S, Snell DB, Madura JD, Surratt CK, Katz JL. Dopamine Transporter Dynamics of N-Substituted Benztropine Analogs with Atypical Behavioral Effects. J Pharmacol Exp Ther. 2018 09; 366(3):527-540.
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Uchida T, Wakasugi M, Kitamura T, Yamamoto T, Asakura M, Fujiwara R, Itoh T, Fujii H, Hirono S. Exploration of DPP-IV inhibitors with a novel scaffold by multistep in silico screening. J Mol Graph Model. 2018 01; 79:254-263.
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Lal P, Cerofolini L, D'Agostino VG, Zucal C, Fuccio C, Bonomo I, Dassi E, Giuntini S, Di Maio D, Vishwakarma V, Preet R, Williams SN, Fairlamb MS, Munk R, Lehrmann E, Abdelmohsen K, Elezgarai SR, Luchinat C, Novellino E, Quattrone A, Biasini E, Manzoni L, Gorospe M, Dixon DA, Seneci P, Marinelli L, Fragai M, Provenzani A. Regulation of HuR structure and function by dihydrotanshinone-I. Nucleic Acids Res. 2017 Sep 19; 45(16):9514-9527.
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Ayyadevara S, Balasubramaniam M, Kakraba S, Alla R, Mehta JL, Shmookler Reis RJ. Aspirin-Mediated Acetylation Protects Against Multiple Neurodegenerative Pathologies by Impeding Protein Aggregation. Antioxid Redox Signal. 2017 Dec 10; 27(17):1383-1396.
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Iyer S, Anwari K, Alsop AE, Yuen WS, Huang DC, Carroll J, Smith NA, Smith BJ, Dewson G, Kluck RM. Identification of an activation site in Bak and mitochondrial Bax triggered by antibodies. Nat Commun. 2016 05 24; 7:11734.
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