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D. Mobley · SciRah

Researcher profile · Semantic Scholar

D. Mobley

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D. Mobley — researcher profile on SciRah

h-index: 58
Works: 203
Citations: 15K

Most-cited papers

Best Practices for Alchemical Free Energy Calculations [Article v1.0]
A. Mey, Bryce K. Allen, Hannah E. Bruce Macdonald, J. Chodera +11 more
2020Living journal of computational molecular science298 citations Open access
Semantic Scholar
Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)
Michael Schauperl, P. Nerenberg, Hyesu Jang, Lee-Ping Wang +3 more
2020Communications Chemistry287 citations Open access
Semantic Scholar
Best Practices for Foundations in Molecular Simulations [Article v1.0]
Efrem Braun, Justin B. Gilmer, H. Mayes, D. Mobley +3 more
2018Living journal of computational molecular science206 citations Open access
Semantic Scholar
Escaping atom types in force fields using direct chemical perception
D. Mobley, Caitlin C. Bannan, A. Rizzi, C. Bayly +8 more
2018Journal of Chemical Theory and Computation171 citations Open access
Semantic Scholar
Development and benchmarking of Open Force Field v1.0.0, the Parsley small molecule force field
Yudong Qiu, Daniel G. A. Smith, Simon Boothroyd, Hyesu Jang +16 more
2020Journal of Chemical Theory and Computation147 citations Open access
Semantic Scholar
Overview of the SAMPL6 host-guest binding affinity prediction challenge
A. Rizzi, Steven L Murkli, J. N. McNeill, Wei Yao +7 more
2018bioRxiv123 citations Open access
Semantic Scholar
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations
A. Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi +13 more
2019bioRxiv101 citations Open access
Semantic Scholar
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge
Teresa Danielle Bergazin, Nicolas Tielker, Ying-Ying Zhang, Jun-Jun Mao +5 more
2021Journal of Computer-Aided Molecular Design81 citations Open access
Semantic Scholar
Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.
Hannes H. Loeffler, S. Bosisio, Guilherme Duarte Ramos Matos, Donghyuk Suh +3 more
2018Journal of Chemical Theory and Computation81 citations Open access
Semantic Scholar
Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]
D. F. Hahn, C. Bayly, Melissa L. Boby, Hannah E. Bruce Macdonald +8 more
2021Living journal of computational molecular science80 citations Open access
Semantic Scholar
Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo
S. Gill, N. Lim, Patrick B. Grinaway, Ariën S. Rustenburg +4 more
2018Journal of Physical Chemistry B68 citations Open access
Semantic Scholar
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge
Mehtap Işık, Teresa Danielle Bergazin, T. Fox, A. Rizzi +2 more
2020bioRxiv62 citations Open access
Semantic Scholar
Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4
L. El Khoury, D. Santos-Martins, Sukanya Sasmal, Jerome Eberhardt +6 more
2019Journal of Computer-Aided Molecular Design62 citations Open access
Semantic Scholar
Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge
Mehtap Işık, D. Levorse, D. Mobley, Timothy Rhodes +1 more
2019bioRxiv59 citations Open access
Semantic Scholar
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale
Joshua T. Horton, S. Boothroyd, J Wagner, J. Mitchell +9 more
2022Journal of Chemical Information and Modeling58 citations Open access
Semantic Scholar
SAMPL7 Host-Guest Challenge Overview: Assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations
Martin Amezcua, L. El Khoury, D. Mobley
2020Journal of Computer-Aided Molecular Design57 citations Open access
Semantic Scholar
Challenges encountered applying equilibrium and non-equilibrium binding free energy calculations
Hannah Baumann, Vytautas Gapsys, B. L. de Groot, D. Mobley
2020Journal of Physical Chemistry B56 citations Open access
Semantic Scholar
Alchemical absolute protein–ligand binding free energies for drug design
Yuriy Khalak, G. Tresadern, Matteo Aldeghi, Hannah Baumann +3 more
2021Chemical Science53 citations Open access
Semantic Scholar
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
Vytautas Gapsys, D. F. Hahn, G. Tresadern, D. Mobley +2 more
2022Journal of Chemical Information and Modeling48 citations Open access
Semantic Scholar
Overview of the SAMPL6 pKa Challenge: Evaluating small molecule microscopic and macroscopic pKa predictions
Mehtap Işık, Ariën S. Rustenburg, A. Rizzi, M. Gunner +2 more
2020bioRxiv47 citations Open access
Semantic Scholar
pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments
Mehtap Işık, D. Levorse, Ariën S. Rustenburg, I. Ndukwe +8 more
2018bioRxiv47 citations Open access
Semantic Scholar
An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA
S. Nainar, B. Cuthbert, N. Lim, W. England +6 more
2020Nature Methods43 citations Open access
Semantic Scholar
Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach
Hannah Baumann, E. Dybeck, Christopher L. McClendon, Frank C. Pickard +6 more
2023Journal of Chemical Theory and Computation41 citations Open access
Semantic Scholar
An overview of the SAMPL8 host–guest binding challenge
Martin Amezcua, Jeffry Setiadi, Yun-Hui Ge, D. Mobley
2022Journal of Computer-Aided Molecular Design41 citations Open access
Semantic Scholar
Benchmark assessment of molecular geometries and energies from small molecule force fields
Victoria T. Lim, D. F. Hahn, G. Tresadern, C. Bayly +1 more
2020F1000Research40 citations Open access
Semantic Scholar
Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods
M. Breznik, Yun-Hui Ge, Joseph P. Bluck, H. Briem +5 more
2022ChemMedChem39 citations Open access
Semantic Scholar
Toward learned chemical perception of force field typing rules
Camila Zanette, Caitlin C. Bannan, C. Bayly, Josh Fass +4 more
2018Journal of Chemical Theory and Computation39 citations Open access
Semantic Scholar
The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation
S. Boothroyd, Lee-Ping Wang, D. Mobley, J. Chodera +1 more
2021Journal of Chemical Theory and Computation38 citations Open access
Semantic Scholar
Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo
Oliver J. Melling, Marley L. Samways, Yun-Hui Ge, D. Mobley +1 more
2023Journal of Chemical Theory and Computation35 citations Open access
Semantic Scholar
Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques
Yun-Hui Ge, David C. Wych, Marley L. Samways, M. E. Wall +2 more
2021bioRxiv35 citations Open access
Semantic Scholar
Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations
M. E. Wall, G. Calabró, C. Bayly, D. Mobley +1 more
2018Journal of the American Chemical Society35 citations Open access
Semantic Scholar
Optimal Designs for Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability
Qingyi Yang, Woodrow Burchett, G. Steeno, Shuai Liu +3 more
2019Journal of Computational Chemistry31 citations Open access
Semantic Scholar
Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative
David R. Slochower, N. M. Henriksen, Lee-Ping Wang, J. Chodera +2 more
2019Journal of Chemical Theory and Computation29 citations Open access
Semantic Scholar
Enhancing Sidechain Rotamer Sampling Using Non-Equilibrium Candidate Monte Carlo
K. Burley, S. Gill, N. Lim, D. Mobley
2018Journal of Chemical Theory and Computation28 citations Open access
Semantic Scholar
Enhancing Water Sampling of Buried Binding Sites Using Nonequilibrium Candidate Monte Carlo
Teresa Danielle Bergazin, I. Ben-Shalom, N. Lim, S. Gill +2 more
2020Journal of Computer-Aided Molecular Design27 citations Open access
Semantic Scholar
Collaborative assessment of molecular geometries and energies from the Open Force Field
Lorenzo D’Amore, D. F. Hahn, David L. Dotson, Joshua T. Horton +15 more
2022Journal of Chemical Information and Modeling26 citations Open access
Semantic Scholar
Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1
D. Mobley, Caitlin C. Bannan, A. Rizzi, C. Bayly +7 more
2018bioRxiv26 citations Open access
Semantic Scholar
Assessing the Conformational Equilibrium of Carboxylic Acid via QM and MD Studies on Acetic Acid
Victoria T. Lim, C. Bayly, L. Fusti-Molnar, D. Mobley
2019Journal of Chemical Information and Modeling25 citations Open access
Semantic Scholar
Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics
Sukanya Sasmal, S. Gill, N. Lim, D. Mobley
2019Journal of Chemical Theory and Computation24 citations Open access
Semantic Scholar
Binding Modes and Metabolism of Caffeine
Z. Jandova, S. Gill, N. Lim, D. Mobley +1 more
2019Chemical Research in Toxicology23 citations Open access
Semantic Scholar
SAMPL6 challenge results from pKa predictions based on a general Gaussian process model
Caitlin C. Bannan, D. Mobley, A. Skillman
2018Journal of Computer-Aided Molecular Design22 citations Open access
Semantic Scholar
Improving force field accuracy by training against condensed phase mixture properties
S. Boothroyd, Owen C Madin, D. Mobley, Lee-Ping Wang +2 more
2021Journal of Chemical Theory and Computation21 citations Open access
Semantic Scholar
Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome
S. Pellegrino, M. Meyer, Zef A. Könst, M. Holm +8 more
2019Nucleic Acids Research20 citations Open access
Semantic Scholar
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction
Harold Grosjean, Mehtap Işık, A. Aimon, D. Mobley +3 more
2022Journal of Computer-Aided Molecular Design19 citations Open access
Semantic Scholar
Improving Small Molecule Force Fields by Identifying and Characterizing Small Molecules with Inconsistent Parameters
Jordan N. Ehrman, Victoria T. Lim, Caitlin C. Bannan, Nam Thi +2 more
2020Journal of Computer-Aided Molecular Design19 citations Open access
Semantic Scholar
Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain
A. Kyrychenko, N. Lim, V. Vasquez-Montes, M. Rodnin +5 more
2018Journal of Membrane Biology18 citations Open access
Semantic Scholar
Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.
Dhiman Ray, T. Gokey, D. Mobley, I. Andricioaei
2020Journal of Chemical Physics17 citations Open access
Semantic Scholar
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations
Yun-Hui Ge, D. F. Hahn, D. Mobley
2021Journal of Chemical Information and Modeling16 citations Open access
Semantic Scholar
D3R Grand Challenge 4: Ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors
Sukanya Sasmal, L. El Khoury, D. Mobley
2019Journal of Computer-Aided Molecular Design16 citations Open access
Semantic Scholar
To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough
M. Pitman, D. F. Hahn, G. Tresadern, D. Mobley
2023Journal of Chemical Information and Modeling15 citations Open access
Semantic Scholar

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