David Lowell Mobley - Publications

Affiliations: 
University of California, Irvine, Irvine, CA 
Area:
Physical chemistry, chemical physics, statistical mechanics, biomolecular simulations, free energy calculations, thermodynamics, molecular dynamics

52 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
2019 Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL. Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. Journal of the American Chemical Society. PMID 30834751 DOI: 10.1021/jacs.8b13613  0.32
2019 Lim VT, Bayly CI, Fusti-Molnar L, Mobley DL. Assessing the conformational equilibrium of carboxylic acid via QM and MD studies on acetic acid. Journal of Chemical Information and Modeling. PMID 30742770 DOI: 10.1021/acs.jcim.8b00835  0.32
2018 Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward learned chemical perception of force field typing rules. Journal of Chemical Theory and Computation. PMID 30512951 DOI: 10.1021/acs.jctc.8b00821  1
2018 Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. Journal of Computer-Aided Molecular Design. PMID 30415285 DOI: 10.1007/s10822-018-0170-6  1
2018 Işık M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD. pK measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. Journal of Computer-Aided Molecular Design. PMID 30406372 DOI: 10.1007/s10822-018-0168-0  1
2018 Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Eastman PK. Escaping atom types in force fields using direct chemical perception. Journal of Chemical Theory and Computation. PMID 30351006 DOI: 10.1021/acs.jctc.8b00640  1
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  0.52
2018 Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. The Journal of Physical Chemistry. B. PMID 29486559 DOI: 10.1021/acs.jpcb.7b11820  1
2017 Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. Journal of Chemical and Engineering Data. 62: 1559-1569. PMID 29056756 DOI: 10.1021/acs.jced.7b00104  1
2017 Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 28752343 DOI: 10.1007/s10822-017-0043-4  0.52
2016 Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 27787702 DOI: 10.1007/s10822-016-9977-1  0.52
2016 Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD. Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. PMID 27718028 DOI: 10.1007/s10822-016-9971-7  1
2016 Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. 30: 927-944. PMID 27677750 DOI: 10.1007/s10822-016-9954-8  0.52
2016 Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? Journal of Computer-Aided Molecular Design. PMID 27658802 DOI: 10.1007/s10822-016-9974-4  0.52
2016 Bannan CC, Calabro G, Kyu DY, Mobley DL. Calculating partition coefficients of small molecules in octanol/water and cyclohexane/water. Journal of Chemical Theory and Computation. PMID 27434695 DOI: 10.1021/acs.jctc.6b00449  0.52
2016 Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL. Using MD simulations to calculate how solvents modulate solubility. Journal of Chemical Theory and Computation. PMID 26878198 DOI: 10.1021/acs.jctc.5b00934  1
2015 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. Journal of Chemical Theory and Computation. 11: 1347. PMID 26579779 DOI: 10.1021/acs.jctc.5b00154  1
2015 Klimovich PV, Shirts MR, Mobley DL. Guidelines for the analysis of free energy calculations. Journal of Computer-Aided Molecular Design. 29: 397-411. PMID 25808134 DOI: 10.1007/s10822-015-9840-9  0.52
2015 Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, ... ... Mobley DL, 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. Journal of the American Chemical Society. 137: 2695-703. PMID 25625324 DOI: 10.1021/ja512751q  1
2014 Parameswaran S, Mobley DL. Box size effects are negligible for solvation free energies of neutral solutes. Journal of Computer-Aided Molecular Design. 28: 825-9. PMID 24976043 DOI: 10.1007/s10822-014-9766-7  1
2014 Fennell CJ, Wymer KL, Mobley DL. A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration Journal of Physical Chemistry B. 118: 6438-6446. PMID 24702668 DOI: 10.1021/jp411529h  1
2014 Mobley DL, Wymer KL, Lim NM, Guthrie JP. Blind prediction of solvation free energies from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 135-50. PMID 24615156 DOI: 10.1007/s10822-014-9718-2  0.48
2014 Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. Blind prediction of HIV integrase binding from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 327-45. PMID 24595873 DOI: 10.1007/s10822-014-9723-5  1
2013 Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. The Journal of Chemical Physics. 139: 184103. PMID 24320250 DOI: 10.1063/1.4826261  1
2013 Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL. Lead optimization mapper: automating free energy calculations for lead optimization. Journal of Computer-Aided Molecular Design. 27: 755-70. PMID 24072356 DOI: 10.1007/s10822-013-9678-y  1
2013 Rocklin GJ, Mobley DL, Dill KA. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. Journal of Chemical Theory and Computation. 9: 3072-3083. PMID 24015114 DOI: 10.1021/ct400315q  1
2013 Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Blind prediction of charged ligand binding affinities in a model binding site. Journal of Molecular Biology. 425: 4569-83. PMID 23896298 DOI: 10.1016/j.jmb.2013.07.030  1
2013 Thaxton A, Izenwasser S, Wade D, Stevens ED, Mobley DL, Jaber V, Lomenzo SA, Trudell ML. 3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters. Bioorganic & Medicinal Chemistry Letters. 23: 4404-7. PMID 23806554 DOI: 10.1016/j.bmcl.2013.05.071  1
2013 Chodera JD, Mobley DL. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annual Review of Biophysics. 42: 121-42. PMID 23654303 DOI: 10.1146/annurev-biophys-083012-130318  1
2013 Rocklin GJ, Mobley DL, Dill KA. Separated topologies--a method for relative binding free energy calculations using orientational restraints. The Journal of Chemical Physics. 138: 085104. PMID 23464180 DOI: 10.1063/1.4792251  1
2013 Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods in Molecular Biology (Clifton, N.J.). 924: 271-311. PMID 23034753 DOI: 10.1007/978-1-62703-017-5_11  0.52
2012 Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE. Alchemical prediction of hydration free energies for SAMPL. Journal of Computer-Aided Molecular Design. 26: 551-62. PMID 22198475 DOI: 10.1007/s10822-011-9528-8  1
2011 Paluch AS, Mobley DL, Maginn EJ. Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. 7: 2910-8. PMID 26605480 DOI: 10.1021/ct200377w  1
2011 Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Current Opinion in Structural Biology. 21: 150-60. PMID 21349700 DOI: 10.1016/j.sbi.2011.01.011  1
2010 Gu X, Izenwasser S, Wade D, Housman A, Gulasey G, Rhoden JB, Savoie CD, Mobley DL, Lomenzo SA, Trudell ML. Synthesis and structure-activity studies of benzyl ester meperidine and normeperidine derivatives as selective serotonin transporter ligands. Bioorganic & Medicinal Chemistry. 18: 8356-64. PMID 20980153 DOI: 10.1016/j.bmc.2010.09.060  1
2010 Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/jp910674d  1
2009 McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. Journal of Chemical Theory and Computation. 5: 2486-2502. PMID 20161451 DOI: 10.1021/ct9001812  1
2009 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. Journal of Chemical Theory and Computation. 5: 350-358. PMID 20150953 DOI: 10.1021/ct800409d  1
2009 Kaur H, Izenwasser S, Verma A, Wade D, Housman A, Stevens ED, Mobley DL, Trudell ML. Synthesis and monoamine transporter affinity of 3alpha-arylmethoxy-3beta-arylnortropanes. Bioorganic & Medicinal Chemistry Letters. 19: 6865-8. PMID 19896846 DOI: 10.1016/j.bmcl.2009.10.087  1
2009 Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. Journal of Molecular Biology. 394: 747-63. PMID 19782087 DOI: 10.1016/j.jmb.2009.09.049  1
2009 Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (London, England : 1993). 17: 489-98. PMID 19368882 DOI: 10.1016/j.str.2009.02.010  1
2009 Mobley DL, Bayly CI, Cooper MD, Dill KA. Predictions of hydration free energies from all-atom molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 4533-7. PMID 19271713 DOI: 10.1021/jp806838b  1
2008 Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. Charge asymmetries in hydration of polar solutes. The Journal of Physical Chemistry. B. 112: 2405-14. PMID 18251538 DOI: 10.1021/jp709958f  1
2008 Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. Journal of Medicinal Chemistry. 51: 769-79. PMID 18215013 DOI: 10.1021/jm070549+  1
2008 Mobley DL, Dill KA, Chodera JD. Treating entropy and conformational changes in implicit solvent simulations of small molecules. The Journal of Physical Chemistry. B. 112: 938-46. PMID 18171044 DOI: 10.1021/jp0764384  1
2007 Mobley DL, Chodera JD, Dill KA. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. Journal of Chemical Theory and Computation. 3: 1231-1235. PMID 18843379 DOI: 10.1021/ct700032n  1
2007 Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. The Journal of Physical Chemistry. B. 111: 13052-63. PMID 17949030 DOI: 10.1021/jp0735987  1
2007 Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology. 371: 1118-34. PMID 17599350 DOI: 10.1016/j.jmb.2007.06.002  1
2007 Mobley DL, Dumont E, Chodera JD, Dill KA. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. The Journal of Physical Chemistry. B. 111: 2242-54. PMID 17291029 DOI: 10.1021/jp0667442  1
2006 Mobley DL, Chodera JD, Dill KA. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. The Journal of Chemical Physics. 125: 084902. PMID 16965052 DOI: 10.1063/1.2221683  1
2004 Mobley DL, Cox DL, Singh RR, Maddox MW, Longo ML. Modeling amyloid beta-peptide insertion into lipid bilayers. Biophysical Journal. 86: 3585-97. PMID 15189856 DOI: 10.1529/biophysj.103.032342  0.56
2003 Mobley DL, Cox DL, Singh RR, Kulkarni RV, Slepoy A. Simulations of oligomeric intermediates in prion diseases. Biophysical Journal. 85: 2213-23. PMID 14507687 DOI: 10.1016/S0006-3495(03)74647-5  0.56
Show low-probability matches.