David L Mobley

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Simulations of oligomeric intermediates in prion diseases
    David L Mobley
    Department of Physics, University of California at Davis, Davis, California, USA
    Biophys J 85:2213-23. 2003
  2. pmc Modeling amyloid beta-peptide insertion into lipid bilayers
    David L Mobley
    Department of Physics, University of California, Davis, California 95616, USA
    Biophys J 86:3585-97. 2004
  3. pmc Blind prediction of HIV integrase binding from the SAMPL4 challenge
    David L Mobley
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 28:327-45. 2014
  4. pmc Lead optimization mapper: automating free energy calculations for lead optimization
    Shuai Liu
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 27:755-70. 2013
  5. pmc Alchemical free energy methods for drug discovery: progress and challenges
    John D Chodera
    California Institute of Quantitative Biosciences QB3, University of California, Berkeley, 260J Stanley Hall, Berkeley, CA 94720, USA
    Curr Opin Struct Biol 21:150-60. 2011
  6. pmc Guidelines for the analysis of free energy calculations
    Pavel V Klimovich
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 29:397-411. 2015
  7. pmc FreeSolv: a database of experimental and calculated hydration free energies, with input files
    David L Mobley
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 28:711-20. 2014
  8. pmc Blind prediction of solvation free energies from the SAMPL4 challenge
    David L Mobley
    Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 28:135-50. 2014
  9. pmc Treating entropy and conformational changes in implicit solvent simulations of small molecules
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    J Phys Chem B 112:938-46. 2008
  10. ncbi request reprint Accurate and efficient corrections for missing dispersion interactions in molecular simulations
    Michael R Shirts
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    J Phys Chem B 111:13052-63. 2007

Collaborators

Detail Information

Publications15

  1. pmc Simulations of oligomeric intermediates in prion diseases
    David L Mobley
    Department of Physics, University of California at Davis, Davis, California, USA
    Biophys J 85:2213-23. 2003
    ..Therefore it can produce some of the same attractive features for the description of prion incubation time data. We propose experiments to test the oligomeric aggregation model...
  2. pmc Modeling amyloid beta-peptide insertion into lipid bilayers
    David L Mobley
    Department of Physics, University of California, Davis, California 95616, USA
    Biophys J 86:3585-97. 2004
    ..These can be used through further experiments to test our hypothesis...
  3. pmc Blind prediction of HIV integrase binding from the SAMPL4 challenge
    David L Mobley
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 28:327-45. 2014
    ..Here, we give an overview of results, highlight some features of methods which worked particularly well, and refer the interested reader to papers in this issue which describe specific submissions for additional details...
  4. pmc Lead optimization mapper: automating free energy calculations for lead optimization
    Shuai Liu
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 27:755-70. 2013
    ..The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license. ..
  5. pmc Alchemical free energy methods for drug discovery: progress and challenges
    John D Chodera
    California Institute of Quantitative Biosciences QB3, University of California, Berkeley, 260J Stanley Hall, Berkeley, CA 94720, USA
    Curr Opin Struct Biol 21:150-60. 2011
    ..In this review, inspired by a recent joint academic/industry meeting organized by the authors, we discuss these challenges and suggest a number of promising approaches for overcoming them...
  6. pmc Guidelines for the analysis of free energy calculations
    Pavel V Klimovich
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 29:397-411. 2015
    ..We hope this tool  and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. ..
  7. pmc FreeSolv: a database of experimental and calculated hydration free energies, with input files
    David L Mobley
    Department of Pharmaceutical Sciences and Department of Chemistry, University of California, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 28:711-20. 2014
    ..In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz . ..
  8. pmc Blind prediction of solvation free energies from the SAMPL4 challenge
    David L Mobley
    Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
    J Comput Aided Mol Des 28:135-50. 2014
    ..We found, however, that in many cases errors are substantially underestimated, and that typically little effort has been invested in estimating likely error. We believe this is an important area for further research. ..
  9. pmc Treating entropy and conformational changes in implicit solvent simulations of small molecules
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
    J Phys Chem B 112:938-46. 2008
    ..03) with the number of rotatable bonds. The present study illustrates that implicit solvent modeling can be improved by eliminating the approximation that solutes are rigid...
  10. ncbi request reprint Accurate and efficient corrections for missing dispersion interactions in molecular simulations
    Michael R Shirts
    Department of Chemistry, Columbia University, New York, New York 10027, USA
    J Phys Chem B 111:13052-63. 2007
    ..In many situations, simulations can be run with even shorter cutoffs than typically used, resulting in increased computational efficiency...
  11. pmc Predicting absolute ligand binding free energies to a simple model site
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143 2518, USA
    J Mol Biol 371:1118-34. 2007
    ..Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved...
  12. ncbi request reprint Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent
    David L Mobley
    Department of Pharmaceutical Chemistry and Graduate Group in Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
    J Phys Chem B 111:2242-54. 2007
    ..Further, we find that the discrepancy with experimental hydration free energies grows substantially with the polarity of the compound, as does its variation across theory levels...
  13. pmc On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
    David L Mobley
    Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
    J Chem Phys 125:084902. 2006
    ..Our method is easily parallelizable, well suited for cases where a ligand cocrystal structure is not available, and can utilize initial orientations generated by docking packages...
  14. ncbi request reprint Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations
    Thomas Steinbrecher
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, San Diego, California 92037, USA
    J Chem Phys 127:214108. 2007
    ..Additionally, results from a more flexible solute, hexane, will also be discussed...
  15. doi request reprint Predicting small-molecule solvation free energies: an informal blind test for computational chemistry
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, New Mexico 87508, USA
    J Med Chem 51:769-79. 2008
    ..6 kcal/mol, with the explicit solvent free energy approach yielding somewhat greater accuracy but at greater computational expense. Insights from outliers and suggestions for future prospective challenges of this kind are presented...