David L. Mobley

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 34

Top Topics

Molecular Dynamics

Top Venues

J. Comput. Aided Mol. Des.

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Hannah M. Baumann, David L. Mobley
Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. J. Comput. Chem. 45 (23, September) (2024)
David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J. Chem. Inf. Model. 64 (13) (2024)
Patrick R. Fitzgerald, Anjali Dixit, Chris Zhang, David L. Mobley, Brian M. Paegel
Building Block-Centric Approach to DNA-Encoded Library Design. J. Chem. Inf. Model. 64 (12) (2024)
Chris Zhang, Mary Pitman, Anjali Dixit, Sumudu Leelananda, Henri Palacci, Meghan Lawler, Svetlana Belyanskaya, Lashadric Grady, Joe Franklin, Nicolas Tilmans, David L. Mobley
Building Block-Based Binding Predictions for DNA-Encoded Libraries. J. Chem. Inf. Model. 63 (16) (2023)
Mary Pitman, David F. Hahn, Gary Tresadern, David L. Mobley
To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. J. Chem. Inf. Model. 63 (6) (2023)
Martin Amezcua, Jeffry Setiadi, Yunhui Ge, David L. Mobley
An overview of the SAMPL8 host-guest binding challenge. J. Comput. Aided Mol. Des. 36 (10) (2022)
Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. J. Comput. Aided Mol. Des. 36 (10) (2022)
Harold Grosjean, Mehtap Isik, Anthony Aimon, David L. Mobley, John D. Chodera, Frank von Delft, Philip C. Biggin
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. J. Comput. Aided Mol. Des. 36 (4) (2022)
Joshua T. Horton, Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David L. Dotson, Pavan Kumar Behara, Venkata Krishnan Ramaswamy, Mark Mackey, John D. Chodera, Jamshed Anwar, David L. Mobley, Daniel J. Cole
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. J. Chem. Inf. Model. 62 (22) (2022)
Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J. Chem. Inf. Model. 62 (5) (2022)
Lorenzo D'amore, David F. Hahn, David L. Dotson, Joshua T. Horton, Jamshed Anwar, Ian Craig, Thomas Fox, Alberto Gobbi, Sirish Kaushik Lakkaraju, Xavier Lucas, Katharina Meier, David L. Mobley, Arjun Narayanan, Christina E. M. Schindler, William C. Swope, Pieter J. in 't Veld, Jeffrey Wagner, Bai Xue, Gary Tresadern
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. J. Chem. Inf. Model. 62 (23) (2022)
Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, Marilyn R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley
, and log D predictions from the SAMPL7 blind challenge. J. Comput. Aided Mol. Des. 35 (7) (2021)
Martin Amezcua, Lea El-Khoury, David L. Mobley
SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J. Comput. Aided Mol. Des. 35 (1) (2021)
Jordan N. Ehrman, Victoria T. Lim, Caitlin C. Bannan, Nam Thi, Daisy Y. Kyu, David L. Mobley
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters. J. Comput. Aided Mol. Des. 35 (3) (2021)
Teresa Danielle Bergazin, Ido Y. Ben-Shalom, Nathan M. Lim, Sam C. Gill, Michael K. Gilson, David L. Mobley
Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J. Comput. Aided Mol. Des. 35 (2) (2021)
Mehtap Isik, Ariën S. Rustenburg, Andrea Rizzi, Marilyn R. Gunner, David L. Mobley, John D. Chodera
predictions. J. Comput. Aided Mol. Des. 35 (2) (2021)
Yunhui Ge, David F. Hahn, David L. Mobley
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. J. Chem. Inf. Model. 61 (3) (2021)
Matthew N. Bahr, Aakankschit Nandkeolyar, John K. Kenna, Neysa Nevins, Luigi Da Vià, Mehtap Isik, John D. Chodera, David L. Mobley
and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. J. Comput. Aided Mol. Des. 35 (11) (2021)
Sukanya Sasmal, Lea El-Khoury, David L. Mobley
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. J. Comput. Aided Mol. Des. 34 (2) (2020)
Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 34 (5) (2020)
Mehtap Isik, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J. Comput. Aided Mol. Des. 34 (4) (2020)
Qingyi Yang, Woodrow Burchett, Gregory S. Steeno, Shuai Liu, Mingjun Yang, David L. Mobley, Xinjun Hou
Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. J. Comput. Chem. 41 (3) (2020)
Mehtap Isik, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J. Comput. Aided Mol. Des. 34 (4) (2020)
Lea El-Khoury, Diogo Santos-Martins, Sukanya Sasmal, Jérôme Eberhardt, Giulia Bianco, Francesca Alessandra Ambrosio, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, David L. Mobley
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. 33 (12) (2019)
Victoria T. Lim, Christopher I. Bayly, Laszlo Fusti-Molnar, David L. Mobley
Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. J. Chem. Inf. Model. 59 (5) (2019)
Caitlin C. Bannan, David L. Mobley, A. Geoffrey Skillman
predictions based on a general Gaussian process model. J. Comput. Aided Mol. Des. 32 (10) (2018)
Andrea Rizzi, Steven Murkli, John N. McNeill, Wei Yao, Matthew R. Sullivan, Michael K. Gilson, Michael Chiu, Lyle Isaacs, Bruce C. Gibb, David L. Mobley, John D. Chodera
Overview of the SAMPL6 host-guest binding affinity prediction challenge. J. Comput. Aided Mol. Des. 32 (10) (2018)
Mehtap Isik, Dorothy Levorse, Ariën S. Rustenburg, Ikenna E. Ndukwe, Heather Wang, Xiao Wang, Mikhail Y. Reibarkh, Gary E. Martin, Alexey A. Makarov, David L. Mobley, Timothy Rhodes, John D. Chodera
pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J. Comput. Aided Mol. Des. 32 (10) (2018)
Maximiliano Riquelme, Alejandro Lara, David L. Mobley, Toon Verstraelen, Adelio R. Matamala, Esteban Vöhringer-Martinez
Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. J. Chem. Inf. Model. 58 (9) (2018)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (8) (2017)
Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson
Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? J. Comput. Aided Mol. Des. 31 (1) (2017)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (1) (2017)
Ariën S. Rustenburg, Justin Dancer, Baiwei Lin, Jianwen A. Feng, Daniel F. Ortwine, David L. Mobley, John D. Chodera
Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. J. Comput. Aided Mol. Des. 30 (11) (2016)
Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J. Comput. Aided Mol. Des. 30 (11) (2016)
Shuai Liu, Lingle Wang, David L. Mobley
Is Ring Breaking Feasible in Relative Binding Free Energy Calculations? J. Chem. Inf. Model. 55 (4) (2015)
Pavel V. Klimovich, Michael R. Shirts, David L. Mobley
Guidelines for the analysis of free energy calculations. J. Comput. Aided Mol. Des. 29 (5) (2015)
David L. Mobley, Daniel M. Zuckerman
A proposal for regularly updated review/survey articles: "Perpetual Reviews". CoRR (2015)
Pavel V. Klimovich, David L. Mobley
A Python tool to set up relative free energy calculations in GROMACS. J. Comput. Aided Mol. Des. 29 (11) (2015)
Hari S. Muddana, Andrew T. Fenley, David L. Mobley, Michael K. Gilson
The SAMPL4 host-guest blind prediction challenge: an overview. J. Comput. Aided Mol. Des. 28 (4) (2014)
David L. Mobley, J. Peter Guthrie
FreeSolv: a database of experimental and calculated hydration free energies, with input files. J. Comput. Aided Mol. Des. 28 (7) (2014)
David L. Mobley, Shuai Liu, Nathan M. Lim, Karisa L. Wymer, Alexander L. Perryman, Stefano Forli, Nan-Jie Deng, Justin Su, Kim Branson, Arthur J. Olson
Blind prediction of HIV integrase binding from the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28 (4) (2014)
David L. Mobley, Karisa L. Wymer, Nathan M. Lim, J. Peter Guthrie
Blind prediction of solvation free energies from the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28 (3) (2014)
Sreeja Parameswaran, David L. Mobley
Box size effects are negligible for solvation free energies of neutral solutes. J. Comput. Aided Mol. Des. 28 (8) (2014)
Thomas S. Peat, Olan Dolezal, Janet Newman, David L. Mobley, John J. Deadman
Interrogating HIV integrase for compounds that bind- a SAMPL challenge. J. Comput. Aided Mol. Des. 28 (4) (2014)
Shuai Liu, Yujie Wu, Teng Lin, Robert Abel, Jonathan P. Redmann, Christopher M. Summa, Vivian R. Jaber, Nathan M. Lim, David L. Mobley
Lead optimization mapper: automating free energy calculations for lead optimization. J. Comput. Aided Mol. Des. 27 (9) (2013)
Pavel V. Klimovich, David L. Mobley
Erratum to: Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J. Comput. Aided Mol. Des. 27 (1) (2013)
David L. Mobley, Shaui Liu, David S. Cerutti, William C. Swope, Julia E. Rice
Alchemical prediction of hydration free energies for SAMPL. J. Comput. Aided Mol. Des. 26 (5) (2012)
David L. Mobley
Let's get honest about sampling. J. Comput. Aided Mol. Des. 26 (1) (2012)
Pavel V. Klimovich, David L. Mobley
Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J. Comput. Aided Mol. Des. 24 (4) (2010)