David L. Mobley

According to our database, David L. Mobley authored at least 50 papers between 2010 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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, Domenico Marson, Pascal T. Merz, Alexander Schlaich, David L. Mobley, Michael R. Shirts, Oliver Beckstein

J. Open Source Softw., 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

Building Block-Centric Approach to DNA-Encoded Library Design.

Patrick R. Fitzgerald, Anjali Dixit, Chris Zhang, David L. Mobley, Brian M. Paegel

J. Chem. Inf. Model., 2024

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

2023

Building Block-Based Binding Predictions for DNA-Encoded Libraries.

Chris Zhang, 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., August, 2023

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., March, 2023

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, Daniel J. Cole

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

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, Arjun Narayanan, Christina E. M. Schindler, William C. Swope, Pieter J. in 't Veld, Jeffrey Wagner, Bai Xue, Gary Tresadern

J. Chem. Inf. Model., 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

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

An overview of the SAMPL8 host-guest binding challenge.

Martin Amezcua, Jeffry Setiadi, Yunhui Ge, David L. Mobley

J. Comput. Aided Mol. Des., 2022

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

Overview of the SAMPL6 pK_a challenge: evaluating small molecule microscopic and macroscopic pK_a predictions.

Mehtap Isik, Ariën S. Rustenburg, Andrea Rizzi, Marilyn R. Gunner, David L. Mobley, John D. Chodera

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

Evaluation of log P, pK_a, 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

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

Automated high throughput pK_a 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

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

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

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

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, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera

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

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

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

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, Stefano Forli, David L. Mobley

J. Comput. Aided Mol. Des., 2019

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

Overview of the SAMPL6 host-guest binding affinity prediction challenge.

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

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

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

2017

Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better?

Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson

J. Comput. Aided Mol. Des., 2017

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong

J. Comput. Aided Mol. Des., 2017

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong

J. Comput. Aided Mol. Des., 2017

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

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

2015

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

Shuai Liu, Lingle Wang, David L. Mobley

J. Chem. Inf. Model., 2015

Guidelines for the analysis of free energy calculations.

Pavel V. Klimovich, Michael R. Shirts, David L. Mobley

J. Comput. Aided Mol. Des., 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

A proposal for regularly updated review/survey articles: "Perpetual Reviews".

David L. Mobley, Daniel M. Zuckerman

CoRR, 2015

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

Box size effects are negligible for solvation free energies of neutral solutes.

Sreeja Parameswaran, David L. Mobley

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

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

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

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

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

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

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

Let's get honest about sampling.

David L. Mobley

J. Comput. Aided Mol. Des., 2012

2010

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