David L Mobley
Affiliation: University of California
- Simulations of oligomeric intermediates in prion diseasesDavid 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...
- Modeling amyloid beta-peptide insertion into lipid bilayersDavid 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...
- Alchemical free energy methods for drug discovery: progress and challengesJohn 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...
- Treating entropy and conformational changes in implicit solvent simulations of small moleculesDavid 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...
- Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solventDavid 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...
- Predicting absolute ligand binding free energies to a simple model siteDavid 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...
- On the use of orientational restraints and symmetry corrections in alchemical free energy calculationsDavid 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...
- Accurate and efficient corrections for missing dispersion interactions in molecular simulationsMichael 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...
- Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculationsThomas 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...
- Predicting small-molecule solvation free energies: an informal blind test for computational chemistryAnthony 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...