David L Mobley

Title(s)Professor, Pharmaceutical Sciences
SchoolSchool of Pharmacy and Pharmaceutical Sciences
Address101 Theory, Suite 100
Irvine CA 92697-3958
Phone(949) 824-6383, 2298
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    Collapse Research 
    Collapse Research Activities and Funding
    Advancing predictive physical modeling through focused development of model systems to drive new modeling innovations
    NIH R01GM124270Sep 10, 2018 - Aug 31, 2022
    Role: Principal Investigator
    Computational alchemy for molecular design and optimization
    NIH R01GM108889Sep 1, 2014 - Aug 31, 2024
    Role: Principal Investigator
    Testing and improving alchemical techniques for predicting protein-ligand binding
    NIH R15GM096257Mar 1, 2012 - Feb 28, 2015
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    1. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. J Chem Theory Comput. 2022 Jun 14; 18(6):3577-3592. Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. PMID: 35533269; PMCID: PMC9254460.
      View in: PubMed   Mentions: 1     Fields:    
    2. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. J Chem Theory Comput. 2022 Jun 14; 18(6):3566-3576. Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. PMID: 35507313; PMCID: PMC9245177.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    3. SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. J Comput Aided Mol Des. 2022 04; 36(4):291-311. Grosjean H, Isik M, Aimon A, Mobley D, Chodera J, von Delft F, Biggin PC. PMID: 35426591; PMCID: PMC9010448.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    4. Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J Chem Inf Model. 2022 03 14; 62(5):1172-1177. Gapsys V, Hahn DF, Tresadern G, Mobley DL, Rampp M, de Groot BL. PMID: 35191702; PMCID: PMC8924919.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    5. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. J Chem Theory Comput. 2022 Mar 08; 18(3):1359-1381. Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. PMID: 35148093; PMCID: PMC9241631.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    6. Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site. Int J Mol Sci. 2021 Nov 23; 22(23). El Khoury L, Mobley DL, Ye D, Rempe SB. PMID: 34884430; PMCID: PMC8657610.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. J Comput Aided Mol Des. 2021 11; 35(11):1141-1155. Bahr MN, Nandkeolyar A, Kenna JK, Nevins N, Da Vià L, Isik M, Chodera JD, Mobley DL. PMID: 34714468; PMCID: PMC9313606.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    8. Alchemical absolute protein-ligand binding free energies for drug design. Chem Sci. 2021 Oct 27; 12(41):13958-13971. Khalak Y, Tresadern G, Aldeghi M, Baumann HM, Mobley DL, de Groot BL, Gapsys V. PMID: 34760182; PMCID: PMC8549785.
      View in: PubMed   Mentions: 2  
    9. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. J Chem Theory Comput. 2021 Oct 12; 17(10):6262-6280. Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. PMID: 34551262; PMCID: PMC8511297.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    10. Temperature artifacts in protein structures bias ligand-binding predictions. Chem Sci. 2021 Sep 01; 12(34):11275-11293. Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. PMID: 34667539; PMCID: PMC8447925.
      View in: PubMed   Mentions: 4  
    11. Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge. J Comput Aided Mol Des. 2021 07; 35(7):771-802. Bergazin TD, Tielker N, Zhang Y, Mao J, Gunner MR, Francisco K, Ballatore C, Kast SM, Mobley DL. PMID: 34169394; PMCID: PMC8224998.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    12. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations. J Phys Chem B. 2021 05 06; 125(17):4241-4261. Baumann HM, Gapsys V, de Groot BL, Mobley DL. PMID: 33905257; PMCID: PMC8240641.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    13. A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. J Chem Inf Model. 2021 03 22; 61(3):1048-1052. Ge Y, Hahn DF, Mobley DL. PMID: 33686853; PMCID: PMC8208087.
      View in: PubMed   Mentions: 3     Fields:    
    14. Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters. J Comput Aided Mol Des. 2021 03; 35(3):271-284. Ehrman JN, Lim VT, Bannan CC, Thi N, Kyu DY, Mobley DL. PMID: 33506360; PMCID: PMC8162916.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    15. SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J Comput Aided Mol Des. 2021 01; 35(1):1-35. Amezcua M, El Khoury L, Mobley DL. PMID: 33392951; PMCID: PMC8121194.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    16. Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions. J Comput Aided Mol Des. 2021 02; 35(2):131-166. Isik M, Rustenburg AS, Rizzi A, Gunner MR, Mobley DL, Chodera JD. PMID: 33394238; PMCID: PMC7904668.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    17. Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target. ACS Infect Dis. 2021 01 08; 7(1):174-188. Burley KH, Cuthbert BJ, Basu P, Newcombe J, Irimpan EM, Quechol R, Foik IP, Mobley DL, Beste DJV, Goulding CW. PMID: 33356117; PMCID: PMC8083904.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    18. Reversibly Sampling Conformations and Binding Modes Using Molecular Darting. J Chem Theory Comput. 2021 Jan 12; 17(1):302-314. Gill SC, Mobley DL. PMID: 33289558; PMCID: PMC8121195.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    19. Benchmark assessment of molecular geometries and energies from small molecule force fields. F1000Res. 2020; 9. Lim VT, Hahn DF, Tresadern G, Bayly CI, Mobley DL. PMID: 33604023; PMCID: PMC7863993.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    20. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning. J Chem Phys. 2020 Oct 21; 153(15):154117. Ray D, Gokey T, Mobley DL, Andricioaei I. PMID: 33092382.
      View in: PubMed   Mentions: 3     Fields:    
    21. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des. 2021 02; 35(2):167-177. Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. PMID: 32968887; PMCID: PMC7904576.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    22. Implementation of a Hospital-Wide Protocol Reduces Time to Decompression and Length of Stay in Patients with Stone-Related Obstructive Pyelonephritis with Sepsis. J Endourol. 2021 01; 35(1):77-83. Haas CR, Smigelski M, Sebesta EM, Mobley D, Shah O. PMID: 32668984.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    23. Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations. Sci Rep. 2020 08 12; 10(1):13587. Lim VT, Geragotelis AD, Lim NM, Freites JA, Tombola F, Mobley DL, Tobias DJ. PMID: 32788614; PMCID: PMC7423955.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    24. Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2). Commun Chem. 2020; 3. Schauperl M, Nerenberg PS, Jang H, Wang LP, Bayly CI, Mobley DL, Gilson MK. PMID: 34136662; PMCID: PMC8204736.
      View in: PubMed   Mentions: 4  
    25. Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations. J Chem Theory Comput. 2020 Apr 14; 16(4):2778-2794. Lim NM, Osato M, Warren GL, Mobley DL. PMID: 32167763; PMCID: PMC7325745.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    26. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J Comput Aided Mol Des. 2020 04; 34(4):335-370. Isik M, Bergazin TD, Fox T, Rizzi A, Chodera JD, Mobley DL. PMID: 32107702; PMCID: PMC7138020.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    27. Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics. J Chem Theory Comput. 2020 Mar 10; 16(3):1854-1865. Sasmal S, Gill SC, Lim NM, Mobley DL. PMID: 32058713; PMCID: PMC7325746.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    28. An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Nat Methods. 2020 03; 17(3):311-318. Nainar S, Cuthbert BJ, Lim NM, England WE, Ke K, Sophal K, Quechol R, Mobley DL, Goulding CW, Spitale RC. PMID: 32015544; PMCID: PMC8518020.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    29. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J Comput Aided Mol Des. 2020 05; 34(5):601-633. 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, Mobley DL, Chodera JD. PMID: 31984465; PMCID: PMC7282318.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    30. Best Practices for Alchemical Free Energy Calculations [Article v1.0]. Living J Comput Mol Sci. 2020; 2(1). 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. PMID: 34458687; PMCID: PMC8388617.
      View in: PubMed   Mentions: 10  
    31. Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J Comput Aided Mol Des. 2020 04; 34(4):405-420. Isik M, Levorse D, Mobley DL, Rhodes T, Chodera JD. PMID: 31858363; PMCID: PMC7301889.
      View in: PubMed   Mentions: 26     Fields:    
    32. Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Struct Dyn. 2019 Nov; 6(6):064704. Wych DC, Fraser JS, Mobley DL, Wall ME. PMID: 31867408; PMCID: PMC6920053.
      View in: PubMed   Mentions: 2  
    33. D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. J Comput Aided Mol Des. 2020 02; 34(2):163-177. Sasmal S, El Khoury L, Mobley DL. PMID: 31781990; PMCID: PMC8208075.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    34. Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. J Comput Chem. 2020 01 30; 41(3):247-257. Yang Q, Burchett W, Steeno GS, Liu S, Yang M, Mobley DL, Hou X. PMID: 31721260; PMCID: PMC6917845.
      View in: PubMed   Mentions: 8     Fields:    
    35. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. J Comput Aided Mol Des. 2019 12; 33(12):1011-1020. El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL. PMID: 31691919; PMCID: PMC7027993.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    36. Structure of a Mycobacterium tuberculosis Heme-Degrading Protein, MhuD, Variant in Complex with Its Product. Biochemistry. 2019 11 19; 58(46):4610-4620. Chao A, Burley KH, Sieminski PJ, de Miranda R, Chen X, Mobley DL, Goulding CW. PMID: 31638374; PMCID: PMC7045704.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    37. Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. J Chem Theory Comput. 2019 Nov 12; 15(11):6225-6242. Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson MK. PMID: 31603667; PMCID: PMC7328435.
      View in: PubMed   Mentions: 7     Fields:    
    38. Binding Modes and Metabolism of Caffeine. Chem Res Toxicol. 2019 07 15; 32(7):1374-1383. Jandova Z, Gill SC, Lim NM, Mobley DL, Oostenbrink C. PMID: 31132250; PMCID: PMC6635882.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    39. Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development. J Chem Theory Comput. 2019 May 14; 15(5):3066-3074. Duarte Ramos Matos G, Calabrò G, Mobley DL. PMID: 30939010; PMCID: PMC6663494.
      View in: PubMed   Mentions: 1     Fields:    
    40. Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome. Nucleic Acids Res. 2019 04 08; 47(6):3223-3232. Pellegrino S, Meyer M, Könst ZA, Holm M, Voora VK, Kashinskaya D, Zanette C, Mobley DL, Yusupova G, Vanderwal CD, Blanchard SC, Yusupov M. PMID: 30759226; PMCID: PMC6451132.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    41. Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. J Am Chem Soc. 2019 03 20; 141(11):4711-4720. Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL. PMID: 30834751; PMCID: PMC6438627.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    42. Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. J Chem Inf Model. 2019 05 28; 59(5):1957-1964. Lim VT, Bayly CI, Fusti-Molnar L, Mobley DL. PMID: 30742770; PMCID: PMC6538459.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    43. Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo. J Chem Theory Comput. 2019 Mar 12; 15(3):1848-1862. Burley KH, Gill SC, Lim NM, Mobley DL. PMID: 30677291; PMCID: PMC6537864.
      View in: PubMed   Mentions: 10     Fields:    
    44. Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput. 2019 Jan 08; 15(1):402-423. Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. PMID: 30512951; PMCID: PMC6467725.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    45. Best Practices for Foundations in Molecular Simulations [Article v1.0]. Living J Comput Mol Sci. 2019; 1(1). Braun E, Gilmer J, Mayes HB, Mobley DL, Monroe JI, Prasad S, Zuckerman DM. PMID: 31788666; PMCID: PMC6884151.
      View in: PubMed   Mentions: 14  
    46. Efficacy and safety of partial splenic embolization for hypersplenism in pre- and post-liver transplant patients: A 16-year comparative analysis. Clin Imaging. 2019 Mar - Apr; 54:71-77. DuBois B, Mobley D, Chick JFB, Srinivasa RN, Wilcox C, Weintraub J. PMID: 30553121.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    47. Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des. 2018 10; 32(10):937-963. Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. PMID: 30415285; PMCID: PMC6301044.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    48. pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J Comput Aided Mol Des. 2018 10; 32(10):1117-1138. Isik M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD. PMID: 30406372; PMCID: PMC6367941.
      View in: PubMed   Mentions: 22     Fields:    
    49. Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput. 2018 Nov 13; 14(11):6076-6092. Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. PMID: 30351006; PMCID: PMC6245550.
      View in: PubMed   Mentions: 29     Fields:    
    50. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. J Chem Theory Comput. 2018 Nov 13; 14(11):5567-5582. Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. PMID: 30289712.
      View in: PubMed   Mentions: 25     Fields:    
    51. SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model. J Comput Aided Mol Des. 2018 10; 32(10):1165-1177. Bannan CC, Mobley DL, Skillman AG. PMID: 30324305; PMCID: PMC6438616.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    52. Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. J Chem Inf Model. 2018 09 24; 58(9):1779-1797. Riquelme M, Lara A, Mobley DL, Verstraelen T, Matamala AR, Vöhringer-Martinez E. PMID: 30125107; PMCID: PMC6195221.
      View in: PubMed   Mentions: 6     Fields:    
    53. Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules. F1000Res. 2018; 7:686. Duarte Ramos Matos G, Mobley DL. PMID: 30109026; PMCID: PMC6069752.
      View in: PubMed   Mentions: 1     Fields:    
    54. Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain. J Membr Biol. 2018 06; 251(3):379-391. Kyrychenko A, Lim NM, Vasquez-Montes V, Rodnin MV, Freites JA, Nguyen LP, Tobias DJ, Mobley DL, Ladokhin AS. PMID: 29550876; PMCID: PMC6030514.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    55. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. J Phys Chem B. 2018 05 31; 122(21):5579-5598. Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL. PMID: 29486559; PMCID: PMC5980761.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    56. Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations. J Chem Theory Comput. 2018 Feb 13; 14(2):759-767. Yang X, Lei H, Gao P, Thomas DG, Mobley DL, Baker NA. PMID: 29293342; PMCID: PMC6906122.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    57. Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. Nat Chem. 2017 12 19; 10(1):8-16. Cremer PS, Flood AH, Gibb BC, Mobley DL. PMID: 29256514.
      View in: PubMed   Mentions: 18     Fields:    
    58. Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 08; 31(8):777. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. PMID: 28752343.
      View in: PubMed   Mentions:    Fields:    
    59. Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides. Nat Chem. 2017 11; 9(11):1140-1149. Könst ZA, Szklarski AR, Pellegrino S, Michalak SE, Meyer M, Zanette C, Cencic R, Nam S, Voora VK, Horne DA, Pelletier J, Mobley DL, Yusupova G, Yusupov M, Vanderwal CD. PMID: 29064494; PMCID: PMC6021127.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    60. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. J Chem Eng Data. 2017 May 11; 62(5):1559-1569. Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. PMID: 29056756; PMCID: PMC5648357.
      View in: PubMed   Mentions: 34  
    61. Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys. 2017 05 22; 46:531-558. Mobley DL, Gilson MK. PMID: 28399632; PMCID: PMC5544526.
      View in: PubMed   Mentions: 90     Fields:    Translation:Cells
    62. Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies. J Phys Chem B. 2017 04 20; 121(15):3458-3472. Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA. PMID: 27966363; PMCID: PMC5398953.
      View in: PubMed   Mentions: 3     Fields:    
    63. A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. Curr Top Med Chem. 2017; 17(23):2577-2585. Abel R, Wang L, Mobley DL, Friesner RA. PMID: 28413950.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    64. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations. Phys Chem Chem Phys. 2016 Nov 30; 18(47):32358-32368. Evoli S, Mobley DL, Guzzi R, Rizzuti B. PMID: 27854368; PMCID: PMC5130592.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    65. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 01; 31(1):147-161. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. PMID: 27787702; PMCID: PMC5581938.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    66. Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):945-958. Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD. PMID: 27718028; PMCID: PMC5209288.
      View in: PubMed   Mentions: 29     Fields:    
    67. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):927-944. Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. PMID: 27677750; PMCID: PMC5209301.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    68. Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des. 2017 01; 31(1):1-19. Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. PMID: 27658802; PMCID: PMC5241188.
      View in: PubMed   Mentions: 72     Fields:    Translation:Cells
    69. Sensitivity in Binding Free Energies Due to Protein Reorganization. J Chem Theory Comput. 2016 Sep 13; 12(9):4620-31. Lim NM, Wang L, Abel R, Mobley DL. PMID: 27462935; PMCID: PMC5021633.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    70. Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water. J Chem Theory Comput. 2016 Aug 09; 12(8):4015-24. Bannan CC, Calabró G, Kyu DY, Mobley DL. PMID: 27434695; PMCID: PMC5053177.
      View in: PubMed   Mentions: 45     Fields:    
    71. Using MD Simulations To Calculate How Solvents Modulate Solubility. J Chem Theory Comput. 2016 Apr 12; 12(4):1930-41. Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL. PMID: 26878198; PMCID: PMC4945102.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    72. A Python tool to set up relative free energy calculations in GROMACS. J Comput Aided Mol Des. 2015 Nov; 29(11):1007-14. Klimovich PV, Mobley DL. PMID: 26487189; PMCID: PMC4749424.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    73. Is ring breaking feasible in relative binding free energy calculations? J Chem Inf Model. 2015 Apr 27; 55(4):727-35. Liu S, Wang L, Mobley DL. PMID: 25835054; PMCID: PMC4489933.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    74. Guidelines for the analysis of free energy calculations. J Comput Aided Mol Des. 2015 May; 29(5):397-411. Klimovich PV, Shirts MR, Mobley DL. PMID: 25808134; PMCID: PMC4420631.
      View in: PubMed   Mentions: 103     Fields:    Translation:Cells
    75. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. J Chem Theory Comput. 2015 Mar 10; 11(3):1347. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. PMID: 26579779; PMCID: PMC4675652.
      View in: PubMed   Mentions: 5     Fields:    
    76. 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. J Am Chem Soc. 2015 Feb 25; 137(7):2695-703. 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, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R. PMID: 25625324.
      View in: PubMed   Mentions: 295     Fields:    Translation:Cells
    77. Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation. J Chem Phys. 2015 Jan 28; 142(4):044508. Paluch AS, Parameswaran S, Liu S, Kolavennu A, Mobley DL. PMID: 25637996; PMCID: PMC4312346.
      View in: PubMed   Mentions: 10     Fields:    
    78. Box size effects are negligible for solvation free energies of neutral solutes. J Comput Aided Mol Des. 2014 Aug; 28(8):825-9. Parameswaran S, Mobley DL. PMID: 24976043.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    79. FreeSolv: a database of experimental and calculated hydration free energies, with input files. J Comput Aided Mol Des. 2014 Jul; 28(7):711-20. Mobley DL, Guthrie JP. PMID: 24928188; PMCID: PMC4113415.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    80. A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration. J Phys Chem B. 2014 Jun 19; 118(24):6438-46. Fennell CJ, Wymer KL, Mobley DL. PMID: 24702668; PMCID: PMC4064691.
      View in: PubMed   Mentions: 23     Fields:    
    81. Blind prediction of solvation free energies from the SAMPL4 challenge. J Comput Aided Mol Des. 2014 Mar; 28(3):135-50. Mobley DL, Wymer KL, Lim NM, Guthrie JP. PMID: 24615156; PMCID: PMC4006301.
      View in: PubMed   Mentions: 80     Fields:    
    82. The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des. 2014 Apr; 28(4):305-17. Muddana HS, Fenley AT, Mobley DL, Gilson MK. PMID: 24599514; PMCID: PMC4053502.
      View in: PubMed   Mentions: 90     Fields:    Translation:Cells
    83. Blind prediction of HIV integrase binding from the SAMPL4 challenge. J Comput Aided Mol Des. 2014 Apr; 28(4):327-45. Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ. PMID: 24595873; PMCID: PMC4331050.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    84. Interrogating HIV integrase for compounds that bind--a SAMPL challenge. J Comput Aided Mol Des. 2014 Apr; 28(4):347-62. Peat TS, Dolezal O, Newman J, Mobley D, Deadman JJ. PMID: 24532034; PMCID: PMC4346355.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    85. 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. J Chem Phys. 2013 Nov 14; 139(18):184103. Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. PMID: 24320250; PMCID: PMC3838431.
      View in: PubMed   Mentions: 67     Fields:    Translation:AnimalsCells
    86. Triazole-dithiocarbamate based selective lysine specific demethylase 1 (LSD1) inactivators inhibit gastric cancer cell growth, invasion, and migration. J Med Chem. 2013 Nov 14; 56(21):8543-60. Zheng YC, Duan YC, Ma JL, Xu RM, Zi X, Lv WL, Wang MM, Ye XW, Zhu S, Mobley D, Zhu YY, Wang JW, Li JF, Wang ZR, Zhao W, Liu HM. PMID: 24131029; PMCID: PMC3881423.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansAnimalsCells
    87. Lead optimization mapper: automating free energy calculations for lead optimization. J Comput Aided Mol Des. 2013 Sep; 27(9):755-70. Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL. PMID: 24072356; PMCID: PMC3837551.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    88. Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol. 2013 Nov 15; 425(22):4569-83. Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. PMID: 23896298; PMCID: PMC3962782.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    89. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. J Chem Theory Comput. 2013 Jul 09; 9(7):3072-3083. Rocklin GJ, Mobley DL, Dill KA. PMID: 24015114; PMCID: PMC3763860.
      View in: PubMed   Mentions: 10     Fields:    
    90. 3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters. Bioorg Med Chem Lett. 2013 Aug 01; 23(15):4404-7. Thaxton A, Izenwasser S, Wade D, Stevens ED, Mobley DL, Jaber V, Lomenzo SA, Trudell ML. PMID: 23806554; PMCID: PMC3733996.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    91. Separated topologies--a method for relative binding free energy calculations using orientational restraints. J Chem Phys. 2013 Feb 28; 138(8):085104. Rocklin GJ, Mobley DL, Dill KA. PMID: 23464180; PMCID: PMC3598757.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    92. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu Rev Biophys. 2013; 42:121-42. Chodera JD, Mobley DL. PMID: 23654303; PMCID: PMC4124006.
      View in: PubMed   Mentions: 114     Fields:    Translation:Cells
    93. An introduction to best practices in free energy calculations. Methods Mol Biol. 2013; 924:271-311. Shirts MR, Mobley DL. PMID: 23034753.
      View in: PubMed   Mentions: 20     Fields:    
    94. Perspective: Alchemical free energy calculations for drug discovery. J Chem Phys. 2012 Dec 21; 137(23):230901. Mobley DL, Klimovich PV. PMID: 23267463; PMCID: PMC3537745.
      View in: PubMed   Mentions: 65     Fields:    Translation:Cells
    95. Alchemical prediction of hydration free energies for SAMPL. J Comput Aided Mol Des. 2012 May; 26(5):551-62. Mobley DL, Liu S, Cerutti DS, Swope WC, Rice JE. PMID: 22198475; PMCID: PMC3583515.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    96. Let's get honest about sampling. J Comput Aided Mol Des. 2012 Jan; 26(1):93-5. Mobley DL. PMID: 22113833.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    97. Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation. J Chem Theory Comput. 2011 Sep 13; 7(9):2910-8. Paluch AS, Mobley DL, Maginn EJ. PMID: 26605480.
      View in: PubMed   Mentions: 7     Fields:    
    98. Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol. 2011 Apr; 21(2):150-60. Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. PMID: 21349700; PMCID: PMC3085996.
      View in: PubMed   Mentions: 196     Fields:    Translation:Cells
    99. Synthesis and structure-activity studies of benzyl ester meperidine and normeperidine derivatives as selective serotonin transporter ligands. Bioorg Med Chem. 2010 Dec 01; 18(23):8356-64. Gu X, Izenwasser S, Wade D, Housman A, Gulasey G, Rhoden JB, Savoie CD, Mobley DL, Lomenzo SA, Trudell ML. PMID: 20980153; PMCID: PMC3713777.
      View in: PubMed   Mentions:    Fields:    
    100. Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J Comput Aided Mol Des. 2010 Apr; 24(4):307-16. Klimovich PV, Mobley DL. PMID: 20372973.
      View in: PubMed   Mentions: 48     Fields:    Translation:Cells
    101. Current status of the AMOEBA polarizable force field. J Phys Chem B. 2010 Mar 04; 114(8):2549-64. 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. PMID: 20136072; PMCID: PMC2918242.
      View in: PubMed   Mentions: 285     Fields:    Translation:Cells
    102. Synthesis and monoamine transporter affinity of 3alpha-arylmethoxy-3beta-arylnortropanes. Bioorg Med Chem Lett. 2009 Dec 15; 19(24):6865-8. Kaur H, Izenwasser S, Verma A, Wade D, Housman A, Stevens ED, Mobley DL, Trudell ML. PMID: 19896846; PMCID: PMC2788963.
      View in: PubMed   Mentions: 2     Fields:    
    103. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol. 2009 Dec 11; 394(4):747-63. Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. PMID: 19782087; PMCID: PMC2788029.
      View in: PubMed   Mentions: 81     Fields:    Translation:Cells
    104. Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput. 2009 Sep 08; 5(9):2486-2502. McClendon CL, Friedland G, Mobley DL, Amirkhani H, Jacobson MP. PMID: 20161451; PMCID: PMC2790287.
      View in: PubMed   Mentions: 94     Fields:    
    105. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure. 2009 Apr 15; 17(4):489-98. Mobley DL, Dill KA. PMID: 19368882; PMCID: PMC2756098.
      View in: PubMed   Mentions: 211     Fields:    Translation:Cells
    106. Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B. 2009 Apr 09; 113(14):4533-7. Mobley DL, Bayly CI, Cooper MD, Dill KA. PMID: 19271713; PMCID: PMC2684682.
      View in: PubMed   Mentions: 33     Fields:    
    107. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput. 2009 Feb 10; 5(2):350-358. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. PMID: 20150953; PMCID: PMC2701304.
      View in: PubMed   Mentions: 123     Fields:    
    108. Charge asymmetries in hydration of polar solutes. J Phys Chem B. 2008 Feb 28; 112(8):2405-14. Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. PMID: 18251538; PMCID: PMC2745216.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    109. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem. 2008 Feb 28; 51(4):769-79. Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. PMID: 18215013.
      View in: PubMed   Mentions: 115     Fields:    
    110. Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B. 2008 Jan 24; 112(3):938-46. Mobley DL, Dill KA, Chodera JD. PMID: 18171044; PMCID: PMC2745223.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    111. Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys. 2007 Dec 07; 127(21):214108. Steinbrecher T, Mobley DL, Case DA. PMID: 18067350.
      View in: PubMed   Mentions: 96     Fields:    Translation:Cells
    112. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B. 2007 Nov 15; 111(45):13052-63. Shirts MR, Mobley DL, Chodera JD, Pande VS. PMID: 17949030.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    113. Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 2007 Aug 24; 371(4):1118-34. Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. PMID: 17599350; PMCID: PMC2104542.
      View in: PubMed   Mentions: 122     Fields:    Translation:Cells
    114. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B. 2007 Mar 08; 111(9):2242-54. Mobley DL, Dumont E, Chodera JD, Dill KA. PMID: 17291029.
      View in: PubMed   Mentions: 97     Fields:    Translation:Cells
    115. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J Chem Theory Comput. 2007; 3(4):1231-1235. Mobley DL, Chodera JD, Dill KA. PMID: 18843379; PMCID: PMC2562444.
      View in: PubMed   Mentions: 85     Fields:    
    116. A mathematical model of glioblastoma tumor spheroid invasion in a three-dimensional in vitro experiment. Biophys J. 2007 Jan 01; 92(1):356-65. Stein AM, Demuth T, Mobley D, Berens M, Sander LM. PMID: 17040992; PMCID: PMC1697862.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansCells
    117. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys. 2006 Aug 28; 125(8):084902. Mobley DL, Chodera JD, Dill KA. PMID: 16965052; PMCID: PMC3583553.
      View in: PubMed   Mentions: 103     Fields:    Translation:Cells
    118. Treatment of a biliary-venous fistula following percutaneous biopsy in a pediatric living related liver transplant patient. Pediatr Radiol. 2006 Jun; 36(6):555-7. Weintraub JL, Hawari A, English B, Mobley D. PMID: 16596368.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    119. Modeling amyloid beta-peptide insertion into lipid bilayers. Biophys J. 2004 Jun; 86(6):3585-97. Mobley DL, Cox DL, Singh RR, Maddox MW, Longo ML. PMID: 15189856; PMCID: PMC1304261.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    120. Simulations of oligomeric intermediates in prion diseases. Biophys J. 2003 Oct; 85(4):2213-23. Mobley DL, Cox DL, Singh RR, Kulkarni RV, Slepoy A. PMID: 14507687; PMCID: PMC1303448.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
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