Abraham MJ, Murtola T, Schulz R, et al. 2015 GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1 219–225
Adewole K, Ishola A, Olaoye 2022 In silico profiling of histone deacetylase inhibitory activity of compounds isolated from Cajanus cajan. Beni-Suef. Univ. J. Basic. Appl. Sci. 11 9
Aihara J 1999 Reduced HOMO−LUMO gap as an index of kinetic stability for polycyclic aromatic hydrocarbons. J. Phys. Chem. A 103 7487–7495
Banavath HN, Sharma OP, Kumar MS, et al. 2014 Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: A virtual screening and molecular dynamics simulations study. Sci. Rep. 4 6948
Article PubMed PubMed Central Google Scholar
Bell EW and Zhang Y 2019 DockRMSD: An open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. J. Cheminform. 11 40
Article PubMed PubMed Central Google Scholar
Bento AP, Hersey A, Félix E, et al. 2020 An open source chemical structure curation pipeline using RDKit. J. Cheminform. 12 51
Article CAS PubMed PubMed Central Google Scholar
Berger A, Venturelli S, Kallnischkies M, et al. 2013 Kaempferol, a new nutrition-derived pan-inhibitor of human histone deacetylases. J. Nutr. Biochem. 24 977–985
Article CAS PubMed Google Scholar
Biasini M, Bienert S, Waterhouse A, et al. 2014 SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42 W252–W258
Article CAS PubMed PubMed Central Google Scholar
Bochevarov AD, Harder E, Hughes TF, et al. 2013 Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences. Int. J. Quantum Chem. 113 2110–2142
Bowie JU, Lüthy R and Eisenberg D 1991 A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 164–170
Article CAS PubMed Google Scholar
Cao Y and Li L 2014 Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model. Bioinformatics 30 1674–1680
Article CAS PubMed Google Scholar
Chen S, Wang X, Cheng Y, et al. 2023 A review of classification, biosynthesis, biological activities and potential applications of flavonoids. Molecules 28 4982
Article CAS PubMed PubMed Central Google Scholar
Childers MC and Daggett V 2018 Validating molecular dynamics simulations against experimental observables in light of underlying conformational ensembles. J. Phys. Chem. B 122 6673–6689
Article CAS PubMed PubMed Central Google Scholar
Colovos C and Yeates TO 1993 Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Sci. 2 1511–1519
Article CAS PubMed PubMed Central Google Scholar
Daina A, Michielin O and Zoete V 2017 SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 7 42717
Article PubMed PubMed Central Google Scholar
Di Giorgio E and Brancolini C 2016 Regulation of class IIa HDAC activities: it is not only matter of subcellular localization. Epigenomics 8 251–269
Dias MC, Pinto D and Silva AMS 2021 Plant flavonoids: Chemical characteristics and biological activity. Molecules 26 5377
Article CAS PubMed PubMed Central Google Scholar
Eberhardt J, Santos-Martins D, Tillack AF, et al. 2021 AutoDock Vina 1.2.0: New docking methods, expanded force field, and Python bindings. J. Chem. Info. Model. 61 3891–3898
Fukui K-i, Yonezawa T and Shingu H 1952 A molecular orbital theory of reactivity in aromatic hydrocarbons. J. Chem. Phys. 20 722–725
Ganai SA 2021 Characterizing binding intensity and energetic features of histone deacetylase inhibitor pracinostat towards class I HDAC isozymes through futuristic drug designing strategy. In Silico Pharmacol. 9 18
Article PubMed PubMed Central Google Scholar
Ganai SA, Farooq Z, Banday S, et al. 2018 In silico approaches for investigating the binding propensity of apigenin and luteolin against class I HDAC isoforms. Future Med. Chem. 10 1925–1945
Article CAS PubMed Google Scholar
Godoy LD, Lucas JE, Bender AJ, et al. 2017 Targeting the epigenome: Screening bioactive compounds that regulate histone deacetylase activity. Mol. Nutr. Food. Res. 61
Graf BA, Milbury PE and Blumberg JB 2005 Flavonols, flavones, flavanones, and human health: epidemiological evidence. J. Med. Food. 8 281–290
Article CAS PubMed Google Scholar
Haberland M, Arnold MA, McAnally J, et al. 2007 Regulation of HDAC9 gene expression by MEF2 establishes a negative-feedback loop in the transcriptional circuitry of muscle differentiation. Mol. Cell. Biol. 27 518–525
Article CAS PubMed Google Scholar
Hawkins PCD, Kelley BP and Warren GL 2014 The application of statistical methods to cognate docking: A path forward? J. Chem. Info. Model. 54 1339–1355
Hess B, Bekker H, Berendsen HJC, et al. 1997 LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18 1463–1472
Hospital A, Goñi JR, Orozco M, et al. 2015 Molecular dynamics simulations: advances and applications. Adv. Appl. Bioinform. Chem. 8 37–47
PubMed PubMed Central Google Scholar
Jablonský M, Štekláč M, Majová V, et al. 2022 Molecular docking and machine learning affinity prediction of compounds identified upon softwood bark extraction to the main protease of the SARS-CoV-2 virus. Biophys. Chem. 288 106854
Article PubMed PubMed Central Google Scholar
Javid R, Dar SA, Mohan S, et al. 2025 Comparative anti-oxidant and anti-inflammatory study of diverse honey types of Kashmir valley through in vitro, analytical chemistry and computational approach. Comput. Biol. Chem. 118 108499
Article CAS PubMed Google Scholar
Kanki K, Watanabe R, Nguyen TL, et al. 2020 HDAC9 is preferentially expressed in dedifferentiated hepatocellular carcinoma cells and is involved in an anchorage-independent growth. Cancers 12 2734
Article CAS PubMed PubMed Central Google Scholar
Kim S, Chen J, Cheng T, et al. 2021 PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Res. 49 D1388–D1395
Article CAS PubMed PubMed Central Google Scholar
Kryshtavych A and Fidelis K 2009 Protein structure prediction and model quality assessment. Drug Discov. Today 14 386–393
Kufareva I and Abagyan R 2012 Methods of protein structure comparison. Methods Mol. Biol. 857 231–257
Article CAS PubMed PubMed Central Google Scholar
Laskowski R, Macarthur MW, Moss DS, et al. 1993 PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 283–291
Li H, Li X, Lin H, et al. 2020 High HDAC9 is associated with poor prognosis and promotes malignant progression in pancreatic ductal adenocarcinoma. Mol. Med. Rep. 21 822–832
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