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Alchemical Free Energy Calculations on Membrane-Associated Proteins.
J Chem Theory Comput. 2023 Nov 14;19(21):7437-7458. doi: 10.1021/acs.jctc.3c00365. Epub 2023 Oct 30.
J Chem Theory Comput. 2023.
PMID: 37902715
Free PMC article.
Review.
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations.
Zavitsanou S, Tsengenes A, Papadourakis M, Amendola G, Chatzigoulas A, Dellis D, Cosconati S, Cournia Z.
Zavitsanou S, et al. Among authors: papadourakis m.
J Chem Inf Model. 2021 Sep 27;61(9):4131-4138. doi: 10.1021/acs.jcim.1c00215. Epub 2021 Sep 14.
J Chem Inf Model. 2021.
PMID: 34519200
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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD.
Rizzi A, et al. Among authors: papadourakis m.
J Comput Aided Mol Des. 2020 May;34(5):601-633. doi: 10.1007/s10822-020-00290-5. Epub 2020 Jan 27.
J Comput Aided Mol Des. 2020.
PMID: 31984465
Free PMC article.
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The effect of S427F mutation on RXRα activity depends on its dimeric partner.
Galdadas I, Bonis V, Vgenopoulou P, Papadourakis M, Kakoulidis P, Stergiou G, Cournia Z, Klinakis A.
Galdadas I, et al. Among authors: papadourakis m.
Chem Sci. 2021 Oct 8;12(44):14700-14710. doi: 10.1039/d1sc04465f. eCollection 2021 Nov 17.
Chem Sci. 2021.
PMID: 34820085
Free PMC article.
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Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin.
Vakali V, Papadourakis M, Georgiou N, Zoupanou N, Diamantis DA, Javornik U, Papakyriakopoulou P, Plavec J, Valsami G, Tzakos AG, Tzeli D, Cournia Z, Mauromoustakos T.
Vakali V, et al. Among authors: papadourakis m.
Molecules. 2022 Aug 26;27(17):5490. doi: 10.3390/molecules27175490.
Molecules. 2022.
PMID: 36080258
Free PMC article.
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Energetics of a protein disorder-order transition in small molecule recognition.
Mendoza-Martinez C, Papadourakis M, Llabrés S, Gupta AA, Barlow PN, Michel J.
Mendoza-Martinez C, et al. Among authors: papadourakis m.
Chem Sci. 2022 Apr 4;13(18):5220-5229. doi: 10.1039/d2sc00028h. eCollection 2022 May 11.
Chem Sci. 2022.
PMID: 35655546
Free PMC article.
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Natural Compounds for Bone Remodeling: A Computational and Experimental Approach Targeting Bone Metabolism-Related Proteins.
Loukas AT, Papadourakis M, Panagiotopoulos V, Zarmpala A, Chontzopoulou E, Christodoulou S, Katsila T, Zoumpoulakis P, Matsoukas MT.
Loukas AT, et al. Among authors: papadourakis m.
Int J Mol Sci. 2024 May 6;25(9):5047. doi: 10.3390/ijms25095047.
Int J Mol Sci. 2024.
PMID: 38732267
Free PMC article.
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Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.
Papadourakis M, Bosisio S, Michel J.
Papadourakis M, et al.
J Comput Aided Mol Des. 2018 Oct;32(10):1047-1058. doi: 10.1007/s10822-018-0154-6. Epub 2018 Aug 29.
J Comput Aided Mol Des. 2018.
PMID: 30159717
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