Preprints/In Press/Perpetual Reviews:

• D. R. Slochower, N. Henriksen, L.-P. Wang, J. D. Chodera, D. L. Mobley, M. K. Gilson, “Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative”, ChemRxiv. Preprint: DOI.
• C. Bannan and D. L. Mobley, “ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns,” ChemRxiv. Preprint: DOI
• D. L. Mobley and M. K. Gilson, “Predicting binding free energies: Frontiers and benchmarks (a perpetual review)”, available on GitHub (latest release; all versions with DOIs). This is the “perpetual review” version of our 2017 Ann. Rev. Biophys. publication and we exercise the right to create derivative works with permission from Annual Review of Biohysics, Volume 46, (c) 2017.
• M. Lim, M. Osato, G. L. Warren and D. L. Mobley, “Fragment Pose Prediction Using Non-Equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations”, ChemRxiv https://doi.org/10.26434/chemrxiv.10032218.v1
• D. R. Slochower, N. Henriksen, L.-P. Wang, J. D. Chodera, D. L. Mobley, M. K. Gilson, “Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative”, ChemRxiv https://doi.org/10.26434/chemrxiv.9159872.v1
• V. T. Lim, A. D. Geragotelis, N. M. Lim, J. A. Freites, F. Tombola, D. L. Mobley, D. Tobias, “Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations”, chemRxiv, DOI

White Papers/Grant Proposals/Other

• D. L. Mobley, M. R. Shirts and D. M. Zuckerman, “Why we need the Living Journal of Computational Molecular Science”, a white paper. (LiveCoMS)
• D. L. Mobley, J. D. Chodera, M. K. Gilson, “Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge community” (2016). (eScholarship)
• D. L. Mobley, J. D. Chodera, L. Isaacs, B. C. Gibb, “Advancing predictive modeling through focused development of model systems to drive new modeling innovations”, an NIH R01 proposal for future SAMPL challenges (2016, revised 2017). (eScholarship)
• D. L. Mobley and D. M. Zuckerman, “A proposal for regularly updated review/survey articles: `Perpetual reviews'”, white paper, (2015). (arXiv, eScholarship).

2020

• Q. Yang, W. Burchett, G. S. Steeno, D. L. Mobley and X. Hou, “Optimal Designs of Pairwise Calculation: An Application to Free Energy Perturbation in Minimizing Prediction Variability”, J. Comp. Chem. 41:247-257 (2020). (Paper: DOI; preprint: DOI).
• S. Sasmal, L. El Khoury, D. L. Mobley, “D3R Grand Challenge 4: Ligand Similarity and MM-GBSA-Based Pose Prediction and Affinity Ranking for BACE-1 Inhibitors”, J. Comput. Aided Mol. Design 34(2):163-177 (2020). (Paper: DOI; preprint: DOI)
• Sasmal, S. C. Gill, N. M. Lim, and D. L. Mobley, “Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo”, J. Chem. Theory Comput. 16(3):1854-1865 (2020). (Paper: DOI; preprint: DOI)
• M. Işık, D. Levorse, D. L. Mobley, T. Rhodes, J. D. Chodera, “Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge”, J. Comput. Aided Mol. Design 34:405-420 (2020). (Paper: DOI, preprint: DOI)
• M. Işık, T. D. Bergazin, T. Fox, A. Rizzi, J. D. Chodera and D. L. Mobley, “Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II logP Challenge”, J. Comput. Aided Mol. Design 34:335-370 (2020). (Paper: DOI)
• S. Nainer, B. J. Cuthbert, N. M. Lim, W. E. England, K. Ke, K. Sophal, R. Quechol, D. L. Mobley, C. W. Goulding, R. C. Spitale, “An optimized chemical-genetic method for cell-specific metabolic labeling of RNA”, Nature Methods 17(3):311-318 (2020). (Paper: DOI)
• Schauperl, P. S. Nerenberg, H. Jang, L.-P. Wang, D. L. Mobley, C. I. Bayly, D. L. Mobley, M. K. Gilson, “Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)”, Communications Chemistry, 3(1):1-11 (2020). (Paper: DOI; preprint: DOI)

2019

• D. C. Wych, J. S. Fraser, D. L. Mobley and M. E. Wall, “Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein”, Structural Dynamics 6:064704 (2019). (Paper: DOI; preprint: DOI)
• Z. Jandova, S. C. Gill, N. M. Lim, D. L. Mobley and C. Oostenbrink, “Binding Modes and Metabolism of Caffeine”, Chem. Res. Toxicol. 32(7):1374-1383 (2019). (Paper: DOI).
• G. D. R. Matos, G. Calabró and D. L. Mobley, “Infinite Dilution Activity Coefficients as Constraints for Force Field Parameterization and Method Development”, J. Chem. Theory Comput. 15(5):3066-3074 (2019). (Preprint: DOI, Paper: DOI)
• Pellegrino, M. Meyer, Z. A. Könst, M. Holm, V. K. Voora, D. Kashinskaya, C. Zanette, G. Yusupova, C. D. Vanderwal, S. C. Blanchard, M. Yusupov, “Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome”, Nucleic Acids Research 47(6):3223-3232 (2019). (Paper: DOI).
• Wall, G. Calabró, C. I. Bayly, D. Mobley, G. Warren. “Biomolecular solvation structure revealed by molecular dynamics simulations,” J. Am. Chem. Soc. 141(11);4711-4720 (2019). (Preprint: DOI ; paper DOI)
• K. H. Burley, S. C. Gill, N. M. Lim and D. L. Mobley, “Enhancing sidechain sampling using non-equilibrium candidate Monte Carlo”, J. Chem. Theory Comput. 15(3):1848-1862 (2019). (preprint DOI, publication DOI)
• V. T. Lim, C. I. Bayly, L. Fusti-Molnar and D. L. Mobley, “Assessing the conformational equilibrium of carboxylic acid via quantum mechanical and molecular dynamics studies on acetic acid,” in press, J. Chem. Inf. Model. (DOI).
• E. Braun, J. Gilmer, H. B. Mayes, D. L. Mobley, J. I. Monroe, S. Prasad, D. M. Zuckerman, “Best practices for foundations in molecular simulations”,  Living Journal of Computational Molecular Science 1(1):5957 (Perpetually updated version: link, Published version: PDF),
• C. Zanette, C. C. Bannan, C. I. Bayly, J. Fass, M. K. Gilson, M. R. Shirts, J. D. Chodera, D. L. Mobley, “Towards Learned Chemical Perception of Force Field Typing Rules”, J. Chem. Theory Comput. 15(1):402-423 (preprint: DOI, publication: DOI).

2018

• D. L. Mobley, C. C. Bannan, A. Rizzi, C. I. Bayly, J. D. Chodera, V. T. Lim, K. A. Beauchamp, D. R. Slochower, M. R. Shirts, M. K. Gilson, and P. K. Eastman, “Escaping atom types in force fields using direct chemical perception”, J. Chem. Theory Comput. 14(11):6076-6092 (2018) (publication: DOI). Recommended by A. MacKerell in F1000 Prime (DOI).
• H. H. Loeffler, S. Bosisio, G. Duarte Ramos Matos, D. Suh, B. Roux, D. L. Mobley, J. Michel, “Reproducibility of free energy calculations across different molecular simulation software”, J. Chem. Theory Comput. 14(11):5567-5582 (preprint: DOI, publication: DOI).
• M. Isik, D. Levorse, A. S. Rustenburg, I. E. Ndukwe, H. Wang, X. Wang, M. Reibarkh, G. E. Martin, A. Makarov, D. L. Mobley, T. Rhodes, J. D. Chodera, “pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments,” J. Comp. Aided Mol. Design 32(10):1117-1138 (Publication: DOI, Preprint: DOI).
• A. Rizzi, S. Murkli, J. N. McNeill, W. Yao, M. Sullivan, M. K. Gilson, M. W. Chiu, L. Isaacs, B. C. Gibb, D. L. Mobley, J. D. Chodera, “Overview of the SAMPL6 host-guest binding affinity prediction challenge”, in press, J. Comp. Aided Mol. Design 32(10):937-963 (preprint: DOI, paper: DOI).
• C. C. Bannan, D. L. Mobley and G. Skillman, “SAMPL6 Challenge Results from pKa Predictions Based on a General Gaussian Process Model,” J. Comp. Aided Mol. Design 32(10):1165-1177 (preprint: DOI, paper: DOI).
• M. Riquelme, A. Lara, D. L. Mobley, T. Verstraelen, A. R. Matamala, and E. Vöhringer-Martinez, “Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field”, J. Chem. Inf. Model. 58(8):1779-1797 (publication: DOI, preprint: DOI).
• D. L. Mobley, C. C. Bannan, A. Rizzi, C. I. Bayly, J. D. Chodera, V. T. Lim, N. M. Lim, K. A. Beauchamp, M. R. Shirts, M. K. Gilson, and P. K. Eastman, “Escaping atom types in force fields using direct chemical perception”, J. Chem. Theory Comput. (DOI)
• G. Duarte Ramos Matos and D. L. Mobley, “Challenges of the use of atomistic simulations to predict solubilities of drug-like molecules”, F1000 Research, May 2018 (DOI).
• S. Gill, N. M. Lim, P. Grinaway, A. S. Rustenburg, J. Fass, J. D. Chodera, D. L. Mobley, “Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo,” in press, J. Phys. Chem. B (DOI, preprint: chemRxiv)
• A. Kyrychenko, N. M. Lim, V. Vasquez-Montes, M. V. Rodnin, J. Alfredo Freites, L. P. Nguyen, D. J. Tobias, D. L. Mobley, A. S. Ladokhin, “Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain,” J. Membrane Biology. (DOI)
• P. S. Cremer, A. H. Flood, B. C. Gibb, and D. L. Mobley, “Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry”, Nature Chemistry 10:8-16 (2018). (DOI)
• X. Yang, H. Lei, P. Gao, D. G. Thomas, D. L. Mobley and N. A. Baker, “Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations,” J. Chem. Theory Comput. 14(2):759-767 (2018) (DOI, arXiv preprint)

2017

• R. Abel, L. Wang, D. L. Mobley and R. A. Friesner, “A critical review of validation, blind testing, and real-world use of alchemical protein-ligand binding free energy calculations,” Current Topics in Medicinal Chemistry 17(23):2577-2585, 2017 (DOI, preprint).
• Z. A. Könst, A. R. Szklarski, S. Pellegrino, S. E. Michalak, M. Meyer, C. Zanette, R. Cencic, Sangkil Nam, V. K. Voora, D. A. Horne, J. Pelletier, D. L. Mobley, G. Yusupova, M. Yusupov and C. D. Vanderwal, “Synthesis facilitates an understanding of the structural basis for translation inhibition by the liccoclimides”, Nature Chemistry. (DOI, free view-only access).
• D. L. Mobley and M. K. Gilson, “Predicting binding free energies: Frontiers and benchmarks”, in Annual Review of Biophysics 46:531-558 (DOI, GitHub)
• Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera, Michael R. Shirts, David L. Mobley, “Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database”, Journal of Chemical and Engineering Data (DOI, eScholarship data)
• L. J. Gosink, C. C. Overall, S. M. Reehl, P. D. Whitney, D. L. Mobley and N. A. Baker, “Bayesian Model Averaging for Ensemble-Based Estimates of Solvation Free Energies” in J. Phys. Chem. B 121(15):3458-3472 (DOI)
• M. R. Shirts, C. Klein, J. M. Swails, J. Yin, M. K. Gilson, D. L. Mobley, D. A. Case, E. D. Zhong, “Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset”, in J. Comput.-Aided Mol. Design 31:147-161 (2017) (DOI)
• J. Yin, N. M. Henriksen, D. R. Slochower, M. R. Shirts, M. W. Chiu, D. L. Mobley and M. K. Gilson, “Overview of the SAMPL5 host-guest challenge: Are we doing better?”, in J. Comput. Aided Mol. Design 31:1-19 (2017). (DOI)

2016

• A. S. Rustenburg, J. Dancer, B. Lin, J. A. Feng, D. F. Ortwine, D. L. Mobley, and J. D. Chodera, “Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge”, in J. Comput.-Aided Mol. Design 30:945-958 (2016). (DOI)
• C. C. Bannan, K. H. Burley, M. Chiu, M. R. Shirts, M. K. Gilson, and D L. Mobley, “Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge”, in J. Comput.-Aided Mol. Design 30:927-944 (2016). (DOI)
• S. Evoli, D. L. Mobley, R. Guzzi, B. Rizzuti, “Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations”, in Physical Chemistry Chemical Physics 18:32358-32368 (2016).  (DOI)
• N. M. Lim, L. Wang, R. Abel, D. L. Mobley, “Sensitivity in binding free energies due to protein reorganization”, in J. Chem. Theory. Comput. 12(9):4620-4631 (2016). (DOI).
• C. C. Bannan, G. Calabro, D. Y. Kyu, D. L. Mobley, “Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water”, in J. Chem. Theory. Comput. 12(8):4015-4024 (2016). (DOI).
• S. Liu, S. Cao, K. Hoang, K. L. Young, A. S. Paluch, D. L. Mobley, “Using MD simulations to calculate how solvents modulate solubility”, in J. Chem. Theory. Comput. 12(4):1930-1941 (2016). (DOI).

2015

• P. V. Klimovich, D. L. Mobley, “A python tool to setup relative free energy calculations in GROMACS”, in J. Comput. Aided. Mol. Design 29(11):1007-1014 (2015). (DOI, Software).
• S. Liu and D. L. Mobley, “Is ring breaking feasible in relative binding free energy calculations?”, in J. Chem. Inf. Model. 55(4):727-735 (2015). (DOI, Supporting trajectory files).
• P. V. Klimovich, M. R. Shirts, and D. L. Mobley, “Guidelines for the analysis of free energy calculations”, in J. Comput. Aided Mol. Design 29(5):397-411 (2015). (DOI, Software)
• L. Wang et al., “Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field”, in J. Am. Chem. Soc.137(7):2695-2703 (2015). (DOI).
• A. S. Paluch, S. Parameswaran, and D. L. Mobley, “Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine and caffeine in binary water/ethanol mixtures via molecular simulation”, in J. Chem. Phys. 142:044508 (2015). (DOI).

2014

• S. Parameswaran and D. L. Mobley, “Box size effects are negligible for solvation free energies of neutral solutes”, J. Comput. Aided Mol. Design., in J. Comput. Aided Mol. Design 28:825-829 (2014). (DOI).
• D. L. Mobley and J. P. Guthrie, “FreeSolv: A database of experimental and calculated hydration free energies, with input files”, in J. Comput. Aided Mol. Design 28(7):711-720 (2014). (DOI, FreeSolv Database, FreeSolv on GitHub).
• C. J. Fennell, K. L. Wymer, and D. L. Mobley, “A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration”, in J. Phys. Chem. B 118(24):6438-6446 (2014). (DOI, hydroxynator on GitHub).
• D. L. Mobley, S. Liu, N. M. Lim, K. L. Wymer, A. L. Perryman, S. Forli, N. Deng, J. Su, K. Branson, A. J. Olson, “Blind prediction of HIV integrase binding from the SAMPL4 challenge”, in J. Comput. Aided Mol. Design 28(4):327-345 (2014) (DOI)
• D. L. Mobley, K. L. Wymer, N. M. Lim, and J. P. Guthrie, “Blind prediction of solvation free energies from the SAMPL4 challenge”, in J. Comput. Aided Mol. Design 28:135-150 (2014) (DOI)
• H. S. Muddana, A. T. Fenley, D. L. Mobley, M. K. Gilson, “The SAMPL4 host-guest blind prediction challenge: an overview”, in J. Comput. Aided Mol. Design 28(4):305-317 (2014) (DOI)
• T. S. Peat, O. Dolezal, J. Newman, D. L. Mobley, J. J. Deadman, “Interrogating HIV integrase for compounds that bind — a SAMPL4 challenge.”, in J. Comput. Aided Mol. Design28:347-362 (2014) (DOI)

2013

• Y-C. Zheng, Y-C. Duan, J.-L. Ma, R.-M. Xu, X. Zi, W.-L. Lv, M.-M. Wang, X.-W. Ye, S. Zhu, D. L. Mobley, Y. Zhu, J.-W. Wang, J.-F. Li, Z.-R. Wang, W. Zhao, H.-M. Zhao, “Triazole-dithiocarbamate based, selective LSD1 inactivators inhibit gastric cancer cell growth, invasion, and migration,” in J. Med. Chem. 56(21):8543-8560 (2013). (DOI)
• G. J. Rocklin, D. L. Mobley, K. A. Dill, and P. H. Hünenberger, “Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for finite-size effects”, in J. Chem. Phys. 139(18):184103 (2013). (DOI). Cover article and highlighted article for J. Chem. Phys. (A talk on the charge correction topic is available on YouTube; it was given to the Gilson and Shen groups by Gabe Rocklin).
• S. Liu, Y. Wu, T. Lin, R. Abel, J. Redmann, C. M. Summa, V. R. Jaber, N. M. Lim, and D. L. Mobley, “Lead Optimization Mapper: Automating free energy calculations for lead optimization”, in J. Comput. Aided Mol. Design 27(9):755-770 (2013). (DOI, LOMAP tool and source code).
• G. J. Rocklin, S. E. Boyce, M. Fisher, I. Fish, D. L. Mobley, B. K. Shoichet, and K. A. Dill, “Blind prediction of charged ligand binding affinities in a model binding site,” J. Mol. Biol.425(22):4569-4583 (2013). (DOI). Highlighted by Faculty of 1000 Prime ().
• A. Thaxton, S. Izenwasser, D. Wade, E. D. Stevens, D. L. Mobley, V. Jaber, S. A. Lomenzo, and M. L. Trudell, “3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters,” in Bioorg. Med. Chem. Lett. 23:4404 (2013). (DOI).
• J. D. Chodera and D. L. Mobley, “Entropy-enthalpy compensation: Role and ramifications in biomolecular ligand recognition and design”, in Ann. Rev. Biophys. 42:141 (2013). (DOI).
• G. J. Rocklin, D. L. Mobley, and K. A. Dill, “Calculating the sensitivity and robustness of binding free energy calculations to force field parameters”, in J. Chem. Theory Comput.9:3072 (2013). (DOI).
• 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. B111:13052-13063 (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 Journal92:356 (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)