18. A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy Calculations
Beierlein, F. B. ; Michel, J. ; Essex, J. W.
J. Phys. Chem. B, 115 (17), 4911 -4926, 2011 doi:10.1021/jp109054j

17. Effects of Water Placement on Predictions of Binding Affinities for p38 MAPalpha Kinase Inhibitors
Lucarelli, J. ; Michel, J. ; Tirado-Rives, J. ; Jorgensen W. L.
J. Chem. Theory Comput., 6 (12), 3850 -3856, 2010 doi:10.1021/ct100504h

Cover article

16. A Remote Arene Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules
Zhang, A. X. ; Murelli, R. P. ; Barinka, C. ; Michel, J. ; Cocleaza, A. ; Jorgensen, W. L. ; Lubkowski, J. ; Spiegel, D. A.
J. Am. Chem. Soc., 132 (36), 12711 -12716, 2010 doi:10.1021/ja104591m
Chemical and Engineering News highlight, Nature Chemical Biology research highlight, Yale University Office of Public Affairs press release

15. Rigorous free energy calculations in structure-based drug design
Michel, J. ; Foloppe, N. ; Essex, J. W.
Mol. Inf., 29, 570 - 578, 2010 doi:10.1002/minf.201000051

14. Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Michel, J. ; Essex, J. W.
J. Comput. Aided Mol. Des., 24 (8), 639 -658 2010 doi:10.1007/s10822-010-9363-3

13. Bridged beta3-Peptide Inhibitors of p53-hDM2 Complexation - Correlation Between Affinity and Cell Permeability
Bautista, A. D. ; Appelbaum, J. S. ; Craig, C. J. ; Michel, J. ; Schepartz, A.
J. Am. Chem. Soc., 132 (9), 2904 -2906, 2010 doi:10.1021/ja910715u

12. Coarse-grain modelling of DMPC and DOPC lipid bilayers
Orsi, M. ; Michel, J. ; Essex, J. W.
J. Phys.: Condens. Matter, 22 (15), 155106, 2010 doi:10.1088/0953-8984/22/15/155106

11. Chemical Control Over Immune Recognition: A Class of Antibody-Recruiting Small Molecules (ARMs) that Target Prostate Cancer
Murelli, R. P. ; Zhang, A. X. ; Michel, J. ; Jorgensen W. L. ; Spiegel, D. A.
J. Am. Chem. Soc., 131 (47), 17090 -17092, 2009 doi:10.1021/ja906844e

Other highlights in Drug Discovery News, Genetic Engineering & Biotechnology, Popular Science, R&D Magazine, e!Science News, Science Daily, Yale University Office of Public Affairs

10. Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization
Michel, J. ; Tirado-Rives, J. ; Jorgensen W. L.
J. Am. Chem. Soc., 131 (42), 15403 -15411, 2009 doi:10.1021/ja906058w

9. Prediction of the water content in protein binding sites
Michel, J. ; Tirado-Rives, J. ; Jorgensen W. L.
J. Phys. Chem. B,113 (40), 13337 -13346, 2009 doi:10.1021/jp9047456

8. In silico improvement of b3-peptide inhibitors of p53•hDM2 and p53•hDMX
Michel, J. ; Harker, E. A. ; Tirado-Rives, J. ; Jorgensen W. L. ; Schepartz, A.
J. Am. Chem. Soc., 131 (18), 6356 -6357, 2009 doi:10.1021/ja901478e

7. Hit identification and binding mode predictions by rigorous free energy simulations
Michel, J. ; Essex, J. W.
J. Med. Chem., 51 (21), 6654 -6664, 2008 doi:10.1021/jm800524s

6. Prediction of partition coefficients by multiscale hybrid atomic level/coarse-grain simulations
Michel, J. ; Orsi, M. ; Essex, J. W.
J. Phys. Chem. B, 112 (3), 657 -660, 2008 doi:10.1021/jp076142y

5. Protein-ligand complexes: computation of the relative free energy of different scaffolds and binding modes
Michel, J. ; Verdonk, M.L ; Essex, J. W.
J. Chem. Theory Comput., 3 (5), 1645 -1655, 2007 doi:10.1021/ct700081t

4. Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?
Michel, J. ; Verdonk, M. L. ; Essex, J. W.
J. Med. Chem. , 49 (25), 7427 -7439, 2006 doi:10.1021/jm061021s

3. The use of free energy simulations as scoring functions
Michel, J.
PhD thesis, University of Southampton, 2006 pdf

2. Efficient generalized Born models for Monte Carlo simulations
Michel, J. ; Taylor, R. D. ; Essex, J. W.
J. Chem. Theory Comput., 2 (3), 732 -739, 2006 doi:10.1021/ct600069r

1. The parameterization and validation of generalized Born models using the pairwise descreening approximation
Michel, J. ; Taylor, R. D. ; Essex, J. W.
J. Comput. Chem., 25, 1760-1770, 2004 doi:10.1002/jcc.20105