David L. Mobley

54 papers Journal 54

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling. J. Chem. Inf. Model. Karmen Condic-Jurkic, Irfan Alibay, Woody Sherman, Mallory R. Tollefson, W. Patrick Walters, Zachary Baker, Lillian T. Chong, Jennifer N. Wei, Jeffrey J. Gray, Brian D. Weitzner, Daniel G. A. Smith, Julia Koehler Leman, Chris Bahl, David L. Mobley
2025	J	`jnl`	The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. J. Chem. Inf. Model. Christian Kramer, John D. Chodera, Kelly L. Damm-Ganamet, Michael K. Gilson, Judith Guenther, Uta F. Lessel, Richard A. Lewis, David L. Mobley, Eva Nittinger, Adam Pecina, Matthieu Schapira, W. Patrick Walters
2024	J	`jnl`	Building Block-Centric Approach to DNA-Encoded Library Design. J. Chem. Inf. Model. Patrick R. Fitzgerald, Anjali Dixit, Chris Zhang, David L. Mobley, Brian M. Paegel
2024	J	`jnl`	Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J. Chem. Inf. Model. David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern
2024	J	`jnl`	Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. J. Comput. Chem. Hannah M. Baumann, David L. Mobley
2024	J	`jnl`	Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling. J. Chem. Inf. Model. Chris Zhang, Meghan Osato, David L. Mobley
2024	J	`jnl`	Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations. J. Chem. Inf. Model. Benjamin Ries, Richard J. Gowers, Hannah M. Baumann, David W. H. Swenson, Michael M. Henry, James R. B. Eastwood, Irfan Alibay, David L. Mobley
2024	J	`jnl`	alchemlyb: the simple alchemistry library. J. Open Source Softw. Zhiyi Wu, David L. Dotson, Irfan Alibay, Bryce K. Allen, Mohammad Soroush Barhaghi, Jérôme Hénin, Thomas T. Joseph, Ian M. Kenney, Hyungro Lee, Haoxi Li, Victoria T. Lim, Shuai Liu, Domenico Marson, Pascal T. Merz, Alexander Schlaich, David L. Mobley, Michael R. Shirts, Oliver Beckstein
2023	J	`jnl`	Building Block-Based Binding Predictions for DNA-Encoded Libraries. J. Chem. Inf. Model. Chris Zhang, Mary Pitman, Anjali Dixit, Sumudu Leelananda, Henri Palacci, Meghan Lawler, Svetlana Belyanskaya, LaShadric Grady, Joe Franklin, Nicolas Tilmans, David L. Mobley
2023	J	`jnl`	To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. J. Chem. Inf. Model. Mary Pitman, David F. Hahn, Gary Tresadern, David L. Mobley
2022	J	`jnl`	An overview of the SAMPL8 host-guest binding challenge. J. Comput. Aided Mol. Des. Martin Amezcua, Jeffry Setiadi, Yunhui Ge, David L. Mobley
2022	J	`jnl`	Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. J. Chem. Inf. Model. 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
2022	J	`jnl`	Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. J. Comput. Aided Mol. Des. Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley
2022	J	`jnl`	Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. J. Chem. Inf. Model. 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
2022	J	`jnl`	Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J. Chem. Inf. Model. Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
2022	J	`jnl`	SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. J. Comput. Aided Mol. Des. Harold Grosjean, Mehtap Isik Bennett, Anthony Aimon, David L. Mobley, John D. Chodera, Frank von Delft, Philip C. Biggin
2021	J	`jnl`	A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. J. Chem. Inf. Model. Yunhui Ge, David F. Hahn, David L. Mobley
2021	J	`jnl`	Automated high throughput pK J. Comput. Aided Mol. Des. Matthew N. Bahr, Aakankschit Nandkeolyar, John K. Kenna, Neysa Nevins, Luigi Da Vià, Mehtap Isik Bennett, John D. Chodera, David L. Mobley
2021	J	`jnl`	Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J. Comput. Aided Mol. Des. Teresa Danielle Bergazin, Ido Y. Ben-Shalom, Nathan M. Lim, Sam C. Gill, Michael K. Gilson, David L. Mobley
2021	J	`jnl`	Evaluation of log P, pK J. Comput. Aided Mol. Des. Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, Marilyn R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley
2021	J	`jnl`	Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters. J. Comput. Aided Mol. Des. Jordan N. Ehrman, Victoria T. Lim, Caitlin C. Bannan, Nam Thi, Daisy Y. Kyu, David L. Mobley
2021	J	`jnl`	Overview of the SAMPL6 pK J. Comput. Aided Mol. Des. Mehtap Isik Bennett, Ariën S. Rustenburg, Andrea Rizzi, Marilyn R. Gunner, David L. Mobley, John D. Chodera
2021	J	`jnl`	SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J. Comput. Aided Mol. Des. Martin Amezcua, Lea El-Khoury, David L. Mobley
2020	J	`jnl`	Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J. Comput. Aided Mol. Des. Mehtap Isik Bennett, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley
2020	J	`jnl`	D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. J. Comput. Aided Mol. Des. Sukanya Sasmal, Lea El-Khoury, David L. Mobley
2020	J	`jnl`	Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J. Comput. Aided Mol. Des. Mehtap Isik Bennett, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera
2020	J	`jnl`	Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. J. Comput. Chem. Qingyi Yang, Woodrow Burchett, Gregory S. Steeno, Shuai Liu, Mingjun Yang, David L. Mobley, Xinjun Hou
2020	J	`jnl`	The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 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
2019	J	`jnl`	Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. J. Chem. Inf. Model. Victoria T. Lim, Christopher I. Bayly, Laszlo Fusti-Molnar, David L. Mobley
2019	J	`jnl`	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. 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
2018	J	`jnl`	Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. J. Chem. Inf. Model. Maximiliano Riquelme, Alejandro Lara, David L. Mobley, Toon Verstraelen, Adelio R. Matamala, Esteban Vöhringer-Martinez
2018	J	`jnl`	Overview of the SAMPL6 host-guest binding affinity prediction challenge. J. Comput. Aided Mol. Des. 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
2018	J	`jnl`	SAMPL6 challenge results from J. Comput. Aided Mol. Des. Caitlin C. Bannan, David L. Mobley, A. Geoffrey Skillman
2018	J	`jnl`	pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J. Comput. Aided Mol. Des. Mehtap Isik Bennett, 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
2017	J	`jnl`	Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017	J	`jnl`	Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017	J	`jnl`	Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? J. Comput. Aided Mol. Des. Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson
2016	J	`jnl`	Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J. Comput. Aided Mol. Des. Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley
2016	J	`jnl`	Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. J. Comput. Aided Mol. Des. Ariën S. Rustenburg, Justin Dancer, Baiwei Lin, Jianwen A. Feng, Daniel F. Ortwine, David L. Mobley, John D. Chodera
2015	J	`jnl`	A Python tool to set up relative free energy calculations in GROMACS. J. Comput. Aided Mol. Des. Pavel V. Klimovich, David L. Mobley
2015	J	`jnl`	A proposal for regularly updated review/survey articles: "Perpetual Reviews". CoRR David L. Mobley, Daniel M. Zuckerman
2015	J	`jnl`	Guidelines for the analysis of free energy calculations. J. Comput. Aided Mol. Des. Pavel V. Klimovich, Michael R. Shirts, David L. Mobley
2015	J	`jnl`	Is Ring Breaking Feasible in Relative Binding Free Energy Calculations? J. Chem. Inf. Model. Shuai Liu, Lingle Wang, David L. Mobley
2014	J	`jnl`	Blind prediction of HIV integrase binding from the SAMPL4 challenge. J. Comput. Aided Mol. Des. 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
2014	J	`jnl`	Blind prediction of solvation free energies from the SAMPL4 challenge. J. Comput. Aided Mol. Des. David L. Mobley, Karisa L. Wymer, Nathan M. Lim, J. Peter Guthrie
2014	J	`jnl`	Box size effects are negligible for solvation free energies of neutral solutes. J. Comput. Aided Mol. Des. Sreeja Parameswaran, David L. Mobley
2014	J	`jnl`	FreeSolv: a database of experimental and calculated hydration free energies, with input files. J. Comput. Aided Mol. Des. David L. Mobley, J. Peter Guthrie
2014	J	`jnl`	Interrogating HIV integrase for compounds that bind- a SAMPL challenge. J. Comput. Aided Mol. Des. Thomas S. Peat, Olan Dolezal, Janet Newman, David L. Mobley, John J. Deadman
2014	J	`jnl`	The SAMPL4 host-guest blind prediction challenge: an overview. J. Comput. Aided Mol. Des. Hari S. Muddana, Andrew T. Fenley, David L. Mobley, Michael K. Gilson
2013	J	`jnl`	Erratum to: Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J. Comput. Aided Mol. Des. Pavel V. Klimovich, David L. Mobley
2013	J	`jnl`	Lead optimization mapper: automating free energy calculations for lead optimization. J. Comput. Aided Mol. Des. Shuai Liu, Yujie Wu, Teng Lin, Robert Abel, Jonathan P. Redmann, Christopher M. Summa, Vivian R. Jaber, Nathan M. Lim, David L. Mobley
2012	J	`jnl`	Alchemical prediction of hydration free energies for SAMPL. J. Comput. Aided Mol. Des. David L. Mobley, Shaui Liu, David S. Cerutti, William C. Swope, Julia E. Rice
2012	J	`jnl`	Let's get honest about sampling. J. Comput. Aided Mol. Des. David L. Mobley
2010	J	`jnl`	Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J. Comput. Aided Mol. Des. Pavel V. Klimovich, David L. Mobley