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Julien Michel - Publications

Affiliations: 
University of Edinburgh, Edinburgh, Scotland, United Kingdom 
Area:
computational chemistry
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58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Herz AM, Kellici T, Morao I, Michel J. Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities. Methods in Molecular Biology (Clifton, N.J.). 2716: 241-264. PMID 37702943 DOI: 10.1007/978-1-0716-3449-3_11  0.384
2023 Hardie A, Cossins BP, Lovera S, Michel J. Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators. Communications Chemistry. 6: 125. PMID 37322137 DOI: 10.1038/s42004-023-00926-1  0.473
2023 Clark F, Robb G, Cole DJ, Michel J. Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation. PMID 37285579 DOI: 10.1021/acs.jctc.3c00139  0.452
2021 Nelson L, Bariami S, Ringrose C, Horton JT, Kurdekar V, Mey ASJS, Michel J, Cole DJ. Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations. Journal of Chemical Information and Modeling. PMID 33886305 DOI: 10.1021/acs.jcim.1c00328  0.455
2020 Mey ASJS, Allen BK, Macdonald HEB, Chodera JD, Hahn DF, Kuhn M, Michel J, Mobley DL, Naden LN, Prasad S, Rizzi A, Scheen J, Shirts MR, Tresadern G, Xu H. Best Practices for Alchemical Free Energy Calculations [Article v1.0]. Living Journal of Computational Molecular Science. 2. PMID 34458687 DOI: 10.33011/livecoms.2.1.18378  0.466
2020 Scheen J, Wu W, Mey ASJS, Tosco P, Mackey MD, Michel J. A hybrid Alchemical Free Energy/Machine Learning Methodology for the Computation of Hydration Free Energies. Journal of Chemical Information and Modeling. PMID 32639733 DOI: 10.1021/Acs.Jcim.0C00600  0.476
2020 Kuhn M, Firth-Clark S, Tosco P, Mey ASJS, Mackey M, Michel J. Assessment of Binding Affinity via Alchemical Free-Energy Calculations. Journal of Chemical Information and Modeling. PMID 32437145 DOI: 10.1021/Acs.Jcim.0C00165  0.458
2020 Kuzmanic A, Bowman GR, Juarez-Jimenez J, Michel J, Gervasio FL. Investigating Cryptic Binding Sites by Molecular Dynamics Simulations. Accounts of Chemical Research. PMID 32134250 DOI: 10.1021/Acs.Accounts.9B00613  0.388
2020 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, et al. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 31984465 DOI: 10.1007/S10822-020-00290-5  0.487
2020 Juárez-Jiménez J, Gupta AA, Karunanithy G, Mey ASJS, Georgiou C, Ioannidis H, Simone AD, Barlow PN, Hulme AN, Walkinshaw MD, Baldwin AJ, Michel J. Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A Chemical Science. 11: 2670-2680. DOI: 10.1039/C9Sc04696H  0.369
2019 Granadino-Roldán JM, Mey ASJS, Pérez González JJ, Bosisio S, Rubio-Martinez J, Michel J. Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors. Plos One. 14: e0213217. PMID 30861030 DOI: 10.1371/Journal.Pone.0213217  0.43
2019 De Simone A, Georgiou C, Ioannidis H, Gupta AA, Juárez-Jiménez J, Doughty-Shenton D, Blackburn EA, Wear MA, Richards JP, Barlow PN, Carragher N, Walkinshaw MD, Hulme AN, Michel J. A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors. Chemical Science. 10: 542-547. PMID 30746096 DOI: 10.2210/Pdb6Gjm/Pdb  0.428
2018 Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software. Journal of Chemical Theory and Computation. PMID 30289712 DOI: 10.1021/Acs.Jctc.8B00544  0.464
2018 Papadourakis M, Bosisio S, Michel J. Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge. Journal of Computer-Aided Molecular Design. PMID 30159717 DOI: 10.1007/S10822-018-0154-6  0.444
2018 Huggins DJ, Biggin PC, Dämgen MA, Essex JW, Harris SA, Henchman RH, Khalid S, Kuzmanic A, Laughton CA, Michel J, Mulholland AJ, Rosta E, Sansom MSP, van der Kamp MW. Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity Wiley Interdisciplinary Reviews: Computational Molecular Science. 9: e1393. DOI: 10.1002/Wcms.1393  0.734
2017 Mey ASJS, Jiménez JJ, Michel J. Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations. Journal of Computer-Aided Molecular Design. PMID 29134431 DOI: 10.1007/S10822-017-0083-9  0.455
2017 Georgiou C, McNae I, Wear M, Ioannidis H, Michel J, Walkinshaw M. Pushing the limits of detection of weak binding using fragment based drug discovery: identification of new cyclophilin binders. Journal of Molecular Biology. PMID 28673552 DOI: 10.1016/J.Jmb.2017.06.016  0.433
2016 Bosisio S, Mey AS, Michel J. Blinded predictions of distribution coefficients in the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. PMID 27677751 DOI: 10.1007/S10822-016-9969-1  0.377
2016 Gerogiokas G, Southey MW, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J. Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory. The Journal of Physical Chemistry. B. PMID 27645529 DOI: 10.1021/Acs.Jpcb.6B07993  0.697
2016 Bosisio S, Mey AS, Michel J. Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. PMID 27503495 DOI: 10.1007/S10822-016-9933-0  0.489
2016 Mey AS, Juárez-Jiménez J, Hennessy A, Michel J. Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge. Bioorganic & Medicinal Chemistry. PMID 27485604 DOI: 10.1016/J.Bmc.2016.07.044  0.429
2016 Calabro G, Woods CJ, Powlesland F, Mey AS, Mulholland AJ, Michel J. Elucidation of Non-Additive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study. The Journal of Physical Chemistry. B. PMID 27248478 DOI: 10.1021/Acs.Jpcb.6B03296  0.478
2016 Bueren-Calabuig JA, Michel J. Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2. Biochemistry. PMID 27050388 DOI: 10.1021/Acs.Biochem.6B00127  0.322
2015 Cuchillo R, Pinto-Gil K, Michel J. A Collective Variable for the Rapid Exploration of Protein Druggability. Journal of Chemical Theory and Computation. 11: 1292-307. PMID 26579775 DOI: 10.1021/Ct501072T  0.458
2015 Mishra SK, Calabró G, Loeffler HH, Michel J, Koča J. Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes. Journal of Chemical Theory and Computation. 11: 3333-45. PMID 26575767 DOI: 10.1021/Acs.Jctc.5B00159  0.471
2015 Loeffler HH, Michel J, Woods C. FESetup: Automating Setup for Alchemical Free Energy Simulations. Journal of Chemical Information and Modeling. PMID 26544598 DOI: 10.1021/Acs.Jcim.5B00368  0.432
2015 Bueren-Calabuig JA, Michel J. Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. Plos Computational Biology. 11: e1004282. PMID 26046940 DOI: 10.1371/Journal.Pcbi.1004282  0.403
2015 Gerogiokas G, Southey MW, Mazanetz MP, Hefeitz A, Bodkin M, Law RJ, Michel J. Correction: Evaluation of water displacement energetics in protein binding sites with grid cell theory. Physical Chemistry Chemical Physics : Pccp. 17: 16213. PMID 26023833 DOI: 10.1039/C5Cp90084K  0.377
2015 Gerogiokas G, Southey MW, Mazanetz MP, Hefeitz A, Bodkin M, Law RJ, Michel J. Evaluation of water displacement energetics in protein binding sites with grid cell theory. Physical Chemistry Chemical Physics : Pccp. 17: 8416-26. PMID 25600031 DOI: 10.1039/C4Cp05572A  0.494
2014 Michel J, Henchman RH, Gerogiokas G, Southey MW, Mazanetz MP, Law RJ. Evaluation of Host-Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory. Journal of Chemical Theory and Computation. 10: 4055-68. PMID 26588549 DOI: 10.1021/Ct500368P  0.704
2014 Gerogiokas G, Calabro G, Henchman RH, Southey MW, Law RJ, Michel J. Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory. Journal of Chemical Theory and Computation. 10: 35-48. PMID 26579889 DOI: 10.1021/Ct400783H  0.7
2014 Woods CJ, Malaisree M, Michel J, Long B, McIntosh-Smith S, Mulholland AJ. Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water. Faraday Discussions. 169: 477-99. PMID 25340314 DOI: 10.1039/C3Fd00125C  0.499
2014 Bodnarchuk MS, Viner R, Michel J, Essex JW. Strategies to calculate water binding free energies in protein-ligand complexes. Journal of Chemical Information and Modeling. 54: 1623-33. PMID 24684745 DOI: 10.1021/Ci400674K  0.682
2014 Michel J. Current and emerging opportunities for molecular simulations in structure-based drug design. Physical Chemistry Chemical Physics : Pccp. 16: 4465-77. PMID 24469595 DOI: 10.1039/C3Cp54164A  0.406
2014 Michel J, Henchman RH, Gerogiokas G, Southey MWY, Mazanetz MP, Law RJ. Evaluation of host-guest binding thermodynamics of model cavities with grid cell theory Journal of Chemical Theory and Computation. 10: 4055-4068. DOI: 10.1021/ct500368p  0.632
2014 Gerogiokas G, Calabro G, Henchman RH, Southey MWY, Law RJ, Michel J. Prediction of small molecule hydration thermodynamics with grid cell theory Journal of Chemical Theory and Computation. 10: 35-48. DOI: 10.1021/ct400783h  0.63
2012 Cuchillo R, Michel J. Mechanisms of small-molecule binding to intrinsically disordered proteins. Biochemical Society Transactions. 40: 1004-8. PMID 22988855 DOI: 10.1042/Bst20120086  0.386
2012 Michel J, Cuchillo R. The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-myc. Plos One. 7: e41070. PMID 22815918 DOI: 10.1371/Journal.Pone.0041070  0.414
2012 Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction. Journal of the American Chemical Society. 134: 4465-8. PMID 22369643 DOI: 10.1021/Ja209924V  0.489
2011 Beierlein FR, Michel J, Essex JW. A simple QM/MM approach for capturing polarization effects in protein-ligand binding free energy calculations. The Journal of Physical Chemistry. B. 115: 4911-26. PMID 21476567 DOI: 10.1021/Jp109054J  0.664
2010 Michel J, Foloppe N, Essex JW. Rigorous Free Energy Calculations in Structure-Based Drug Design. Molecular Informatics. 29: 570-8. PMID 27463452 DOI: 10.1002/Minf.201000051  0.672
2010 Orsi M, Michel J, Essex JW. Coarse-grain modelling of DMPC and DOPC lipid bilayers. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 22: 155106. PMID 21389551 DOI: 10.1088/0953-8984/22/15/155106  0.576
2010 Luccarelli J, Michel J, Tirado-Rives J, Jorgensen WL. Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors. Journal of Chemical Theory and Computation. 6: 3850-3856. PMID 21278915 DOI: 10.1021/Ct100504H  0.608
2010 Zhang AX, Murelli RP, Barinka C, Michel J, Cocleaza A, Jorgensen WL, Lubkowski J, Spiegel DA. A remote arene-binding site on prostate specific membrane antigen revealed by antibody-recruiting small molecules. Journal of the American Chemical Society. 132: 12711-6. PMID 20726553 DOI: 10.1021/Ja104591M  0.488
2010 Michel J, Essex JW. Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. Journal of Computer-Aided Molecular Design. 24: 639-58. PMID 20509041 DOI: 10.1007/S10822-010-9363-3  0.664
2010 Michel J, Foloppe N, Essex JW. Rigorous free energy calculations in structure-based drug design Molecular Informatics. 29: 570-578. DOI: 10.1002/minf.201000051  0.552
2009 Murelli RP, Zhang AX, Michel J, Jorgensen WL, Spiegel DA. Chemical control over immune recognition: a class of antibody-recruiting small molecules that target prostate cancer. Journal of the American Chemical Society. 131: 17090-2. PMID 19888723 DOI: 10.1021/Ja906844E  0.455
2009 Michel J, Tirado-Rives J, Jorgensen WL. Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization. Journal of the American Chemical Society. 131: 15403-11. PMID 19778066 DOI: 10.1021/Ja906058W  0.618
2009 Michel J, Tirado-Rives J, Jorgensen WL. Prediction of the water content in protein binding sites. The Journal of Physical Chemistry. B. 113: 13337-46. PMID 19754086 DOI: 10.1021/Jp9047456  0.623
2009 Michel J, Harker EA, Tirado-Rives J, Jorgensen WL, Schepartz A. In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX. Journal of the American Chemical Society. 131: 6356-7. PMID 19415930 DOI: 10.1021/Ja901478E  0.428
2008 Michel J, Essex JW. Hit identification and binding mode predictions by rigorous free energy simulations. Journal of Medicinal Chemistry. 51: 6654-64. PMID 18834104 DOI: 10.1021/Jm800524S  0.668
2008 Michel J, Orsi M, Essex JW. Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. The Journal of Physical Chemistry. B. 112: 657-60. PMID 18163606 DOI: 10.1021/Jp076142Y  0.594
2007 Michel J, Verdonk ML, Essex JW. Protein-Ligand Complexes:  Computation of the Relative Free Energy of Different Scaffolds and Binding Modes. Journal of Chemical Theory and Computation. 3: 1645-55. PMID 26627610 DOI: 10.1021/Ct700081T  0.662
2007 Michel J, Verdonk ML, Essex JW. Protein-ligand complexes: Computation of the relative free energy of different scaffolds and binding modes Journal of Chemical Theory and Computation. 3: 1645-1655. DOI: 10.1021/ct700081t  0.589
2006 Michel J, Taylor RD, Essex JW. Efficient Generalized Born Models for Monte Carlo Simulations. Journal of Chemical Theory and Computation. 2: 732-9. PMID 26626678 DOI: 10.1021/Ct600069R  0.639
2006 Michel J, Verdonk ML, Essex JW. Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization? Journal of Medicinal Chemistry. 49: 7427-39. PMID 17149872 DOI: 10.1021/Jm061021S  0.676
2006 Michel J, Taylor RD, Essex JW. Efficient generalized born models for Monte Carlo simulations Journal of Chemical Theory and Computation. 2: 732-739. DOI: 10.1021/ct600069r  0.526
2004 Michel J, Taylor RD, Essex JW. The parameterization and validation of generalized born models using the pairwise descreening approximation. Journal of Computational Chemistry. 25: 1760-70. PMID 15362133 DOI: 10.1002/Jcc.20105  0.634
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