Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. - Pavel V. Klimovich; David L. Mobley (J. Comput. Aided Mol. Des., 2010)

Let's get honest about sampling. - David L. Mobley (J. Comput. Aided Mol. Des., 2012)

Alchemical prediction of hydration free energies for SAMPL. - David L. Mobley; Shaui Liu; David S. Cerutti; William C. Swope; Julia E. Rice (J. Comput. Aided Mol. Des., 2012)

Erratum to: Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. - Pavel V. Klimovich; David L. Mobley (J. Comput. Aided Mol. Des., 2013)

Lead optimization mapper: automating free energy calculations for lead optimization. - Shuai Liu; Yujie Wu; Teng Lin; Robert Abel; Jonathan P. Redmann; Christopher M. Summa; Vivian R. Jaber; Nathan M. Lim; David L. Mobley (J. Comput. Aided Mol. Des., 2013)

FreeSolv: a database of experimental and calculated hydration free energies, with input files. - David L. Mobley; J. Peter Guthrie (J. Comput. Aided Mol. Des., 2014)

Blind prediction of HIV integrase binding from the SAMPL4 challenge. - 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 (J. Comput. Aided Mol. Des., 2014)

Blind prediction of solvation free energies from the SAMPL4 challenge. - David L. Mobley; Karisa L. Wymer; Nathan M. Lim; J. Peter Guthrie (J. Comput. Aided Mol. Des., 2014)

The SAMPL4 host-guest blind prediction challenge: an overview. - Hari S. Muddana; Andrew T. Fenley; David L. Mobley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2014)

Box size effects are negligible for solvation free energies of neutral solutes. - Sreeja Parameswaran; David L. Mobley (J. Comput. Aided Mol. Des., 2014)

Interrogating HIV integrase for compounds that bind- a SAMPL challenge. - Thomas S. Peat; Olan Dolezal; Janet Newman; David L. Mobley; John J. Deadman (J. Comput. Aided Mol. Des., 2014)

A proposal for regularly updated review/survey articles: "Perpetual Reviews". - David L. Mobley; Daniel M. Zuckerman (CoRR, 2015)

A Python tool to set up relative free energy calculations in GROMACS. - Pavel V. Klimovich; David L. Mobley (J. Comput. Aided Mol. Des., 2015)

Guidelines for the analysis of free energy calculations. - Pavel V. Klimovich; Michael R. Shirts; David L. Mobley (J. Comput. Aided Mol. Des., 2015)

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations? - Shuai Liu; Lingle Wang; David L. Mobley (J. Chem. Inf. Model., 2015)

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. - Caitlin C. Bannan; Kalistyn H. Burley; Michael Chiu; Michael R. Shirts; Michael K. Gilson; David L. Mobley (J. Comput. Aided Mol. Des., 2016)

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. - Ariën S. Rustenburg; Justin Dancer; Baiwei Lin; Jianwen A. Feng; Daniel F. Ortwine; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2016)

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? - Jian Yin 005; Niel M. Henriksen; David R. Slochower; Michael R. Shirts; Michael Chiu; David L. Mobley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2017)

SAMPL6 challenge results from a predictions based on a general Gaussian process model. - Caitlin C. Bannan; David L. Mobley; A. Geoffrey Skillman (J. Comput. Aided Mol. Des., 2018)

pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. - 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 (J. Comput. Aided Mol. Des., 2018)

Overview of the SAMPL6 host-guest binding affinity prediction challenge. - Andrea Rizzi; Steven Murkli; John N. McNeill; Wei Yao 010; Matthew R. Sullivan; Michael K. Gilson; Michael Chiu; Lyle Isaacs; Bruce C. Gibb; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2018)

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. - Maximiliano Riquelme; Alejandro Lara; David L. Mobley; Toon Verstraelen; Adelio R. Matamala; Esteban Vöhringer-Martinez (J. Chem. Inf. Model., 2018)

Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. - Lea El-Khoury; Diogo Santos-Martins; Sukanya Sasmal; Jérôme Eberhardt; Giulia Bianco; Francesca Alessandra Ambrosio; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; David L. Mobley (J. Comput. Aided Mol. Des., 2019)

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. - Victoria T. Lim; Christopher I. Bayly; Laszlo Fusti-Molnar; David L. Mobley (J. Chem. Inf. Model., 2019)

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. - Mehtap Isik; Teresa Danielle Bergazin; Thomas Fox; Andrea Rizzi; John D. Chodera; David L. Mobley (J. Comput. Aided Mol. Des., 2020)

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. - Mehtap Isik; Dorothy Levorse; David L. Mobley; Timothy Rhodes; John D. Chodera (J. Comput. Aided Mol. Des., 2020)

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. - 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; et al. (J. Comput. Aided Mol. Des., 2020)

D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors. - Sukanya Sasmal; Lea El-Khoury; David L. Mobley (J. Comput. Aided Mol. Des., 2020)

Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability. - Qingyi Yang; Woodrow Burchett; Gregory S. Steeno; Shuai Liu; Mingjun Yang; David L. Mobley; Xinjun Hou (J. Comput. Chem., 2020)

SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. - Martin Amezcua; Lea El-Khoury; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. - Matthew N. Bahr; Aakankschit Nandkeolyar; John K. Kenna; Neysa Nevins; Luigi Da Vià; Mehtap Isik; John D. Chodera; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. - Teresa Danielle Bergazin; Ido Y. Ben-Shalom; Nathan M. Lim; Sam C. Gill; Michael K. Gilson; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge. - Teresa Danielle Bergazin; Nicolas Tielker; Yingying Zhang; Junjun Mao; Marilyn R. Gunner; Karol Francisco; Carlo Ballatore; Stefan M. Kast; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

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; Daisy Y. Kyu; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions. - Mehtap Isik; Ariën S. Rustenburg; Andrea Rizzi; Marilyn R. Gunner; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2021)

A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. - Yunhui Ge; David F. Hahn; David L. Mobley (J. Chem. Inf. Model., 2021)

An overview of the SAMPL8 host-guest binding challenge. - Martin Amezcua; Jeffry Setiadi; Yunhui Ge; David L. Mobley (J. Comput. Aided Mol. Des., 2022)

Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. - Yunhui Ge; Oliver J. Melling; Weiming Dong; Jonathan W. Essex; David L. Mobley (J. Comput. Aided Mol. Des., 2022)

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. - Harold Grosjean; Mehtap Isik; Anthony Aimon; David L. Mobley; John D. Chodera; Frank von Delft; Philip C. Biggin (J. Comput. Aided Mol. Des., 2022)

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. - 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; et al. (J. Chem. Inf. Model., 2022)

Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. - Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot (J. Chem. Inf. Model., 2022)

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. - 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; et al. (J. Chem. Inf. Model., 2022)

To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. - Mary Pitman; David F. Hahn; Gary Tresadern; David L. Mobley (J. Chem. Inf. Model., 2023)

Building Block-Based Binding Predictions for DNA-Encoded Libraries. - Chris Zhang 002; Mary Pitman; Anjali Dixit; Sumudu Leelananda; Henri Palacci; Meghan Lawler; Svetlana Belyanskaya; Lashadric Grady; Joe Franklin; Nicolas Tilmans; David L. Mobley (J. Chem. Inf. Model., 2023)

Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. - Hannah M. Baumann; David L. Mobley (J. Comput. Chem., 2024)

Building Block-Centric Approach to DNA-Encoded Library Design. - Patrick R. Fitzgerald; Anjali Dixit; Chris Zhang 002; David L. Mobley; Brian M. Paegel (J. Chem. Inf. Model., 2024)

Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. - David F. Hahn; Vytautas Gapsys; Bert L. de Groot; David L. Mobley; Gary Tresadern (J. Chem. Inf. Model., 2024)

Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations. - Benjamin Ries; Richard J. Gowers; Hannah M. Baumann; David W. H. Swenson; Michael M. Henry; James R. B. Eastwood; Irfan Alibay; David L. Mobley (J. Chem. Inf. Model., 2024)

Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling. - Chris Zhang 002; Meghan Osato; David L. Mobley (J. Chem. Inf. Model., 2024)

alchemlyb: the simple alchemistry library. - 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; et al. (J. Open Source Softw., 2024)

alchemlyb. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

alchemlyb: the simple alchemistry library. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

alchemlyb: the simple alchemistry library. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. - 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 (J. Chem. Inf. Model., 2025)