 Molecular Docking Simulation
"Molecular Docking 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 technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
| Descriptor ID |
D062105
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| MeSH Number(s) |
E05.599.595.249 L01.224.160.249
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| Concept/Terms |
Molecular Docking Simulation- Molecular Docking Simulation
- Docking Simulation, Molecular
- Docking Simulations, Molecular
- Simulation, Molecular Docking
- Simulations, Molecular Docking
- Molecular Docking Simulations
Molecular Docking Analysis- Molecular Docking Analysis
- Analyses, Molecular Docking
- Analysis, Molecular Docking
- Docking Analyses, Molecular
- Docking Analysis, Molecular
- Molecular Docking Analyses
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Below are MeSH descriptors whose meaning is more general than "Molecular Docking Simulation".
Below are MeSH descriptors whose meaning is more specific than "Molecular Docking Simulation".
This graph shows the total number of publications written about "Molecular Docking Simulation" by people in UAMS Profiles by year, and whether "Molecular Docking 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 |
|---|
| 2023 | 0 | 4 | 4 | | 2022 | 0 | 1 | 1 | | 2021 | 1 | 5 | 6 | | 2020 | 1 | 3 | 4 | | 2019 | 1 | 1 | 2 | | 2018 | 0 | 2 | 2 | | 2017 | 0 | 3 | 3 | | 2016 | 0 | 3 | 3 | | 2015 | 1 | 4 | 5 | | 2014 | 1 | 2 | 3 | | 2013 | 0 | 2 | 2 |
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Below are the most recent publications written about "Molecular Docking Simulation" by people in Profiles over the past ten years.
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Boateng ST, Roy T, Torrey K, Owunna U, Banang-Mbeumi S, Basnet D, Niedda E, Alexander AD, Hage DE, Atchimnaidu S, Nagalo BM, Aryal D, Findley A, Seeram NP, Efimova T, Sechi M, Hill RA, Ma H, Chamcheu JC, Murru S. Synthesis, in silico modelling, and in?vitro biological evaluation of substituted pyrazole derivatives as potential anti-skin cancer, anti-tyrosinase, and antioxidant agents. J Enzyme Inhib Med Chem. 2023 Dec; 38(1):2205042.
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Wang X, DeFilippis RA, Weldemichael T, Gunaganti N, Tran P, Leung YK, Shah NP, Li HY. An imidazo[1,2-a]pyridine-pyridine derivative potently inhibits FLT3-ITD and FLT3-ITD secondary mutants, including gilteritinib-resistant FLT3-ITD/F691L. Eur J Med Chem. 2024 Jan 15; 264:115977.
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Zhang D, Hong L, Zhang RS, Zhang Q, Yao J, Wang J, Zhang N. Identification of the key mechanisms of action of Si-Ni-San in uveitis using bioinformatics and network pharmacology. Medicine (Baltimore). 2023 Aug 25; 102(34):e34615.
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Ganne A, Balasubramaniam M, Ayyadevara H, Kiaei L, Shmookler Reis RJ, Varughese KI, Kiaei M. In silico analysis of TUBA4A mutations in Amyotrophic Lateral Sclerosis to define mechanisms of microtubule disintegration. Sci Rep. 2023 02 06; 13(1):2096.
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Tomar A, Sahoo S, Aathi M, Kuila S, Khan MA, Ravi GRR, Jeyaraman J, Mehta JL, Varughese KI, Arockiasamy A. Exploring the druggability of oxidized low-density lipoprotein (ox-LDL) receptor, LOX-1, a proatherogenic drug target involved in atherosclerosis. Biochem Biophys Res Commun. 2022 10 01; 623:59-65.
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Kueakulpattana N, Wannigama DL, Luk-In S, Hongsing P, Hurst C, Badavath VN, Jenjaroenpun P, Wongsurawat T, Teeratakulpisan N, Kerr SJ, Abe S, Phattharapornjaroen P, Shein AMS, Saethang T, Chantaravisoot N, Amarasiri M, Higgins PG, Chatsuwan T. Multidrug-resistant Neisseria gonorrhoeae infection in heterosexual men with reduced susceptibility to ceftriaxone, first report in Thailand. Sci Rep. 2021 11 04; 11(1):21659.
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Moiani D, Link TM, Brosey CA, Katsonis P, Lichtarge O, Kim Y, Joachimiak A, Ma Z, Kim IK, Ahmed Z, Jones DE, Tsutakawa SE, Tainer JA. An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. Methods Enzymol. 2021; 661:407-431.
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Sadr AS, Abdollahpour Z, Aliahmadi A, Eslahchi C, Nekouei M, Kiaei L, Kiaei M, Ghassempour A. Detection of structural and conformational changes in ALS-causing mutant profilin-1 with hydrogen/deuterium exchange mass spectrometry and bioinformatics techniques. Metab Brain Dis. 2022 01; 37(1):229-241.
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Penthala NR, Balasubramaniam M, Dachavaram SS, Morris EJ, Bhat-Nakshatri P, Ponder J, Jordan CT, Nakshatri H, Crooks PA. Antitumor properties of novel sesquiterpene lactone analogs as NF?B inhibitors that bind to the IKK? ubiquitin-like domain (ULD). Eur J Med Chem. 2021 Nov 15; 224:113675.
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Vyskocil S, Cardin D, Ciavarri J, Conlon J, Cullis C, England D, Gershman R, Gigstad K, Gipson K, Gould A, Greenspan P, Griffin R, Gulavita N, Harrison S, Hu Z, Hu Y, Hata A, Huang J, Huang SC, Janowick D, Jones M, Kolev V, Langston SP, Lee HM, Li G, Lok D, Ma L, Mai D, Malley J, Matsuda A, Mizutani H, Mizutani M, Molchanova N, Nunes E, Pusalkar S, Renou C, Rowland S, Sato Y, Shaw M, Shen L, Shi Z, Skene R, Soucy F, Stroud S, Xu H, Xu T, Abu-Yousif AO, Zhang J. Identification of Novel Carbocyclic Pyrimidine Cyclic Dinucleotide STING Agonists for Antitumor Immunotherapy Using Systemic Intravenous Route. J Med Chem. 2021 05 27; 64(10):6902-6923.
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Mishra GP, Bhadane RN, Panigrahi D, Amawi HA, Asbhy CR, Tiwari AK. The interaction of the bioflavonoids with five SARS-CoV-2 proteins targets: An in silico study. Comput Biol Med. 2021 07; 134:104464.
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Sadr AS, Eslahchi C, Ghassempour A, Kiaei M. In silico studies reveal structural deviations of mutant profilin-1 and interaction with riluzole and edaravone in amyotrophic lateral sclerosis. Sci Rep. 2021 03 25; 11(1):6849.
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Yan W, Zhang L, Lv F, Moccia M, Carlomagno F, Landry C, Santoro M, Gosselet F, Frett B, Li HY. Discovery of pyrazolo-thieno[3,2-d]pyrimidinylamino-phenyl acetamides as type-II pan-tropomyosin receptor kinase (TRK) inhibitors: Design, synthesis, and biological evaluation. Eur J Med Chem. 2021 Apr 15; 216:113265.
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Klejborowska G, Urbaniak A, Maj E, Wietrzyk J, Moshari M, Preto J, Tuszynski JA, Chambers TC, Huczynski A. Synthesis, anticancer activity and molecular docking studies of N-deacetylthiocolchicine and 4-iodo-N-deacetylthiocolchicine derivatives. Bioorg Med Chem. 2021 02 15; 32:116014.
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Roy T, Boateng ST, Banang-Mbeumi S, Singh PK, Basnet P, Chamcheu RN, Ladu F, Chauvin I, Spiegelman VS, Hill RA, Kousoulas KG, Nagalo BM, Walker AL, Fotie J, Murru S, Sechi M, Chamcheu JC. Synthesis, inverse docking-assisted identification and in vitro biological characterization of Flavonol-based analogs of fisetin as c-Kit, CDK2 and mTOR inhibitors against melanoma and non-melanoma skin cancers. Bioorg Chem. 2021 02; 107:104595.
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Balasubramaniam M, Mainali N, Bowroju SK, Atluri P, Penthala NR, Ayyadevera S, Crooks PA, Shmookler Reis RJ. Structural modeling of GSK3? implicates the inactive (DFG-out) conformation as the target bound by TDZD analogs. Sci Rep. 2020 10 27; 10(1):18326.
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Yang JF, Williams AH, Penthala NR, Prather PL, Crooks PA, Zhan CG. Binding Modes and Selectivity of Cannabinoid 1 (CB1) and Cannabinoid 2 (CB2) Receptor Ligands. ACS Chem Neurosci. 2020 10 21; 11(20):3455-3463.
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Klejborowska G, Urbaniak A, Maj E, Preto J, Moshari M, Wietrzyk J, Tuszynski JA, Chambers TC, Huczynski A. Synthesis, biological evaluation and molecular docking studies of new amides of 4-chlorothiocolchicine as anticancer agents. Bioorg Chem. 2020 04; 97:103664.
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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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Klejborowska G, Urbaniak A, Preto J, Maj E, Moshari M, Wietrzyk J, Tuszynski JA, Chambers TC, Huczynski A. Synthesis, biological evaluation and molecular docking studies of new amides of 4-bromothiocolchicine as anticancer agents. Bioorg Med Chem. 2019 12 01; 27(23):115144.
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Majcher U, Urbaniak A, Maj E, Moshari M, Delgado M, Wietrzyk J, Bartl F, Chambers TC, Tuszynski JA, Huczynski A. Synthesis, antiproliferative activity and molecular docking of thiocolchicine urethanes. Bioorg Chem. 2018 12; 81:553-566.
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Zafar MK, Maddukuri L, Ketkar A, Penthala NR, Reed MR, Eddy S, Crooks PA, Eoff RL. A Small-Molecule Inhibitor of Human DNA Polymerase ? Potentiates the Effects of Cisplatin in Tumor Cells. Biochemistry. 2018 02 20; 57(7):1262-1273.
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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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Parcon PA, Balasubramaniam M, Ayyadevara S, Jones RA, Liu L, Shmookler Reis RJ, Barger SW, Mrak RE, Griffin WST. Apolipoprotein E4 inhibits autophagy gene products through direct, specific binding to CLEAR motifs. Alzheimers Dement. 2018 02; 14(2):230-242.
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Stepan AF, Claffey MM, Reese MR, Balan G, Barreiro G, Barricklow J, Bohanon MJ, Boscoe BP, Cappon GD, Chenard LK, Cianfrogna J, Chen L, Coffman KJ, Drozda SE, Dunetz JR, Ghosh S, Hou X, Houle C, Karki K, Lazzaro JT, Mancuso JY, Marcek JM, Miller EL, Moen MA, O'Neil S, Sakurada I, Skaddan M, Parikh V, Smith DL, Trapa P, Tuttle JB, Verhoest PR, Walker DP, Won A, Wright AS, Whritenour J, Zasadny K, Zaleska MM, Zhang L, Shaffer CL. Discovery and Characterization of (R)-6-Neopentyl-2-(pyridin-2-ylmethoxy)-6,7-dihydropyrimido[2,1-c][1,4]oxazin-4(9H)-one (PF-06462894), an Alkyne-Lacking Metabotropic Glutamate Receptor 5 Negative Allosteric Modulator Profiled in both Rat and Nonhuman Primates. J Med Chem. 2017 09 28; 60(18):7764-7780.
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Janganati V, Ponder J, Thakkar S, Jordan CT, Crooks PA. Succinamide derivatives of melampomagnolide B and their anti-cancer activities. Bioorg Med Chem. 2017 07 15; 25(14):3694-3705.
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Allison D, Delancey E, Ramey H, Williams C, Alsharif ZA, Al-Khattabi H, Ontko A, Gilmore D, Alam MA. Synthesis and antimicrobial studies of novel derivatives of 4-(4-formyl-3-phenyl-1H-pyrazol-1-yl)benzoic acid as potent anti-Acinetobacter baumannii agents. Bioorg Med Chem Lett. 2017 02 01; 27(3):387-392.
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Xi JB, Fang YF, Frett B, Zhu ML, Zhu T, Kong YN, Guan FJ, Zhao Y, Zhang XW, Li HY, Ma ML, Hu W. Structure-based design and synthesis of imidazo[1,2-a]pyridine derivatives as novel and potent Nek2 inhibitors with in?vitro and in?vivo antitumor activities. Eur J Med Chem. 2017 Jan 27; 126:1083-1106.
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Madadi NR, Ketkar A, Penthala NR, Bostian AC, Eoff RL, Crooks PA. Dioxol and dihydrodioxin analogs of 2- and 3-phenylacetonitriles as potent anti-cancer agents with nanomolar activity against a variety of human cancer cells. Bioorg Med Chem Lett. 2016 May 01; 26(9):2164-9.
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Rajagopalan P, Alahmari KA, Elbessoumy AA, Balasubramaniam M, Suresh R, Shariff ME, Chandramoorthy HC. Biological evaluation of 2-arylidene-4, 7-dimethyl indan-1-one (FXY-1): a novel Akt inhibitor with potent activity in lung cancer. Cancer Chemother Pharmacol. 2016 Feb; 77(2):393-404.
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Penthala NR, Ketkar A, Sekhar KR, Freeman ML, Eoff RL, Balusu R, Crooks PA. 1-Benzyl-2-methyl-3-indolylmethylene barbituric acid derivatives: Anti-cancer agents that target nucleophosmin 1 (NPM1). Bioorg Med Chem. 2015 Nov 15; 23(22):7226-33.
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Hidayat AN, Aki-Yalcin E, Beksac M, Tian E, Usmani SZ, Ertan-Bolelli T, Yalcin I. Insight into human protease activated receptor-1 as anticancer target by molecular modelling. SAR QSAR Environ Res. 2015; 26(10):795-807.
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Madadi NR, Penthala NR, Howk K, Ketkar A, Eoff RL, Borrelli MJ, Crooks PA. Synthesis and biological evaluation of novel 4,5-disubstituted 2H-1,2,3-triazoles as cis-constrained analogues of combretastatin A-4. Eur J Med Chem. 2015 Oct 20; 103:123-32.
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Penthala NR, Thakkar S, Crooks PA. Heteroaromatic analogs of the resveratrol analog DMU-212 as potent anti-cancer agents. Bioorg Med Chem Lett. 2015 Jul 15; 25(14):2763-7.
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Franco FM, Jones DE, Harris PK, Han Z, Wildman SA, Jarvis CM, Janetka JW. Structure-based discovery of small molecule hepsin and HGFA protease inhibitors: Evaluation of potency and selectivity derived from distinct binding pockets. Bioorg Med Chem. 2015 May 15; 23(10):2328-43.
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Penthala NR, Zong H, Ketkar A, Madadi NR, Janganati V, Eoff RL, Guzman ML, Crooks PA. Synthesis, anticancer activity and molecular docking studies on a series of heterocyclic trans-cyanocombretastatin analogues as antitubulin agents. Eur J Med Chem. 2015 Mar 06; 92:212-20.
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