Preprints/In Press
- S. Liu, Y. Wu, T. Lin, R. Abel, J. Redmann, C. M. Summa, and D. L. Mobley, "Lead Optimization Mapper: Automating free energy calculations for lead optimization", submitted.(PDF preprint).
- G. J. Rocklin, D. L. Mobley, and K. A. Dill, "Calculating the sensitivity and robustness of binding free energy calculations to force field parameters", submitted. (PDF preprint).
- J. D. Chodera and D. L. Mobley, "Entropy-enthalpy compensation: Role and ramifications in biomolecular ligand recognition and design", forthcoming. (PDF preprint).
2013
- G. J. Rocklin, D. L. Mobley, and K. A. Dill, "Separated topologies—A method for relative binding free energy calculations using orientational restraints", in J. Chem. Phys. 138:085104 (2013). (DOI).
- M. R. Shirts and D. L. Mobley, "An introduction to best practices in free energy calculations", in Biomolecular Simulations: Methods and Protocols, Methods in Molecular Biology 924:271-311 (2013). (DOI.)
2012
- D. L. Mobley and P. V. Klimovich, "Perspective: Alchemical free energy calculations for drug discovery", Journal of Chemical Physics, 137:230901 (2012) (DOI (free full text)).
- D. L. Mobley, S. Liu, D. Cerutti, W. C. Swope, and J. E. Rice, "Alchemical prediction of hydration free energies for SAMPL", Journal of Computer-Aided Molecular Design, 26(5): 551-562 (2012).(DOI.)
- D. L. Mobley, "Let's get honest about sampling", Journal of Computer-Aided Molecular Design perspective, 26(1):93-95 (2012) (DOI, PDF).
2011
- C. D. Savoie and D. L. Mobley, "Understanding the structural and functional effects of mutations in HIV-1 protease mutants using 100 ns molecular dynamics simulations", Journal of Computational Science Education, 2(1): 28-34 (2011). (PDF).
- A. S. Paluch, D. L. Mobley, and E. J. Maginn, "Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation", Journal of Chemical Theory and Computation 7:2910-2918 (2011). (DOI, PDF).
- J. D. Chodera, D. L. Mobley, M. R. Shirts, R. W. Dixon, K. Branson, V. S. Pande, "Alchemical free energy methods for drug discovery: Progress and challenges", Current Opinion in Structural Biology 21:150-160 (2011). (DOI).
2010
- X. Gu, S. Izenwasser, D. Wade, A. Housman, G. Gulasey, J. B. Rhoden, C. D. Savoie, D. L. Mobley, S. A. Lomenzo, and M. D. Trudell. "Synthesis and Structure-Activity Studies of Benzyl Ester Meperidine and Normeperidine Derivatives as Selective Serotonin Transporter Ligands", Bioorg. Med. Chem. Lett. 18: 8356-8364, 2010. (DOI)
- P. V. Klimovich and D. L. Mobley, "Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations", J. Computer-Aided Molecular Design 24: 307-316 (2010). (DOI)
- M. R. Shirts, D. L. Mobley and S. P. Brown, "Free energy calculations in structure-based drug design", in "Drug Design: Structure- and Ligand-Based Approaches", Cambridge University Press (2010), edited by Kenneth M. Merz, Dagmar Ringe and Charles H. Reynolds. Invited chapter.
- J. Ponder, C. Wu, V. Pande, J. Chodera, M. Schneiders, D. Mobley, I. Haque, D. Lambrecht, R. Distasio, Jr., M. Head-Gordon, G. Clark, M. Johnson, T. Head-Gordon. "Current status of the AMOEBA polarizable force field", J. Phys. Chem. B. 114: 2549-2564 (2010). (Cover article). (DOI)
2009
- H. Kaur, S. Izenwasser, A. Verma, D. Wade, A. Housman, E. D. Stevens, D. L. Mobley, and M. L. Trudell. "Synthesis and monoamine transporter affinity of 3alpha-Arylmethoxy-3beta-arylnortropanes", Bioorg. Med. Chem. Lett. 10:6865-6868 (2009). (DOI)
- S. E. Boyce, D. L. Mobley, G. Rocklin, A. P. Graves, K. A. Dill, B. K. Shoichet. "Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site", J. Mol. Biol. 394: 747-763 (2009). (DOI).
- C. L. McClendon, G. Friedman, D. L. Mobley, H. Amirkhani, J. P. Nilmeier, and M. P. Jacobson, "Thermodynamically significant correlated motions couple allosteric binding sites in human Interleukin-2", J. Chem. Theory Comput. 5 (9): 2486-2502 (2009). (DOI).
- D. L. Mobley and K. A. Dill, "The binding of small-molecule ligands to proteins: 'What you see' is not always 'what you get'", Structure 17(4): 489-498 (2009). (DOI)
- D. L. Mobley, C. I. Bayly, M. D. Cooper, and K. A. Dill, "Predictions of hydration free energies from all-atom molecular dynamics simulations", J. Phys. Chem. B 113: 4533-4537 (2009). Invited article, special issue on "Calculation of Aqueous Solvation Energies of Drug-Like Molecules: A Blind Challenge". (DOI).
- D. L. Mobley, C. I. Bayly, M. D. Cooper, M. R. Shirts, and K. A. Dill. "Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge force fields", J. Chem. Theory Comput. 5: 350-358 (2009). One of the top 10 most downloaded articles from March 2008 to March 2009. One of the top 20 most downloaded articles in 2009. (DOI, supporting info, mol2 files with partial charges, parameter and coordinate files).
Previous work
2008
- D. L. Mobley, A. Barber II, C. Fennell, and K. A. Dill. "Charge asymmetries in hydration of polar solutes", J. Phys. Chem. B 112: 2405-2414, 2008. (DOI). See also erratum by D. L.Mobley, J. R. Baker, A. Barber II, C. Fennell, and K. A. Dill, 115:1545 (2011). (DOI)
- A. Nicholls, D. L. Mobley, J. P. Guthrie, J. D. Chodera, C. I. Bayly, M. D. Cooper, and V. S. Pande. "Predicting small-molecule solvation free energies: a blind challenge test for computational chemistry", J. Med. Chem. 51: 769-779 (2008). (DOI).
- D. L. Mobley, J. D. Chodera, and K. A. Dill. "Entropy and conformational change in implicit solvent simulations of small molecules", J. Phys. Chem. B 112:938-946 (2008). (DOI, supporting information, small molecule test set, stored Amber trajectories (600 MB)).
2007
- T. Steinbrecher, D. L. Mobley, and D. A. Case. "Non-linear scaling schemes for Lennard-Jones interactions in free energy calculations", J. Chem. Phys. 127: 214108 (2007). (DOI).
- M. R. Shirts, D. L. Mobley, and J. D. Chodera. "Alchemical free energy calculations: Ready for prime time?", Annual Reports in Computational Chemistry 3:41-59 (2007). (DOI).
- M. R. Shirts, D. L. Mobley, J. D. Chodera, and V. S. Pande. "Accurate and efficient corrections for missing dispersion interactions in molecular simulations", J. Phys. Chem. B 111:13052-13063 (2007). (DOI).
- D. L. Mobley, J. D. Chodera, and K. A. Dill, "Confine and Release: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change", Journal of Chemical Theory and Computation 3(4):1231-1235 (2007). (DOI)
- D. L. Mobley, A. P. Graves, J. D. Chodera, A. C. McReynolds, B. K. Shoichet and K. A. Dill, "Predicting absolute ligand binding free energies to a simple model site," Journal of Molecular Biology 371(4):1118-1134 (2007). (DOI).
- D. L. Mobley, E. Dumont, J. D. Chodera and K. A. Dill", "Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent", J. Phys. Chem. B. 111:2242-2254 (2007). (DOI). See also erratum, 115:1329-1332 (2011). (DOI)
- A. M. Stein, T. Demuth, D. Mobley, M. Berens, and L. Sander. "A Mathematical Model of Glioblastoma Tumor Spheroid Invasion in a 3-D in vitro Experiment", Biophysical Journal 92:356 (2007). (DOI)
2006
- D. L. Mobley, J. D. Chodera, K. A. Dill. "On the use of orientational restraints and symmetry number corrections in alchemical free energy calculations", Journal of Chemical Physics 125:084902, 2006. Selected for the Virtual Journal of Biological Physics Research 12(5), 2006. (DOI)
2004
- D. L. Mobley, D. L. Cox, R. R. P. Singh, M. W. Maddox, M. L. Longo. "Modeling Amyloid Beta Peptide Insertion into Lipid Bilayers", Biophysical Journal 86, 3585-3597, 2004. (DOI)
- D. L. Mobley, "Models of Cooperative Dynamics from Biomolecules to Magnets". Dissertation, University of California, Davis, July 2004
- D. L. Mobley, C. R. Pike, J. E. Davies, D. L. Cox, R. R. P. Singh, "Hysteresis loops of Co-Pt perpendicular magnetic multilayers", Journal of Physics: Condensed Matter 16, 5897-5906, 2004. (DOI)
2003
- D. L. Mobley, D. L. Cox, R. R. P. Singh, R. V. Kulkarni and A. Slepoy. "Simulations of Oligomeric Intermediates in Prion Diseases", Biophysical Journal 85, 2213-2223, 2003. (DOI)