Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

por Duarte Ramos Matos, Guilherme, Mobley, David L.
Publicado 2019

A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration

por Fennell, Christopher J., Wymer, Karisa L., Mobley, David L.
Publicado 2014

An overview of the SAMPL8 host–guest binding challenge

por Amezcua, Martin, Setiadi, Jeffry, Ge, Yunhui, Mobley, David L.
Publicado 2022

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

por Wych, David C., Fraser, James S., Mobley, David L., Wall, Michael E.
Publicado 2019

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

por El Khoury, Léa, Mobley, David L., Ye, Dongmei, Rempe, Susan B.
Publicado 2021

PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSM

por Smith, Louis G., Novak, Borna, Osato, Meghan, Mobley, David L., Bowman, Gregory R.
Publicado 2023

A transferable double exponential potential for condensed phase simulations of small molecules

por Horton, Joshua T., Boothroyd, Simon, Behara, Pavan Kumar, Mobley, David L., Cole, Daniel J.
Publicado 2023

Binding Modes and Metabolism of Caffeine

por Jandova, Zuzana, Gill, Samuel C., Lim, Nathan M., Mobley, David L., Oostenbrink, Chris
Publicado 2019

Benchmark assessment of molecular geometries and energies from small molecule force fields

por Lim, Victoria T., Hahn, David F., Tresadern, Gary, Bayly, Christopher I., Mobley, David L.
Publicado 2020

Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo

por Melling, Oliver J., Samways, Marley L., Ge, Yunhui, Mobley, David L., Essex, Jonathan W.
Publicado 2023

Temperature artifacts in protein structures bias ligand-binding predictions

por Bradford, Shanshan Y. C., El Khoury, Léa, Ge, Yunhui, Osato, Meghan, Mobley, David L., Fischer, Marcus
Publicado 2021

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

por Gapsys, Vytautas, Hahn, David F., Tresadern, Gary, Mobley, David L., Rampp, Markus, de Groot, Bert L.
Publicado 2022

Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)

por Schauperl, Michael, Nerenberg, Paul S., Jang, Hyesu, Wang, Lee-Ping, Bayly, Christopher I., Mobley, David L., Gilson, Michael K.
Publicado 2020

Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations

por Lim, Victoria T., Geragotelis, Andrew D., Lim, Nathan M., Freites, J. Alfredo, Tombola, Francesco, Mobley, David L., Tobias, Douglas J.
Publicado 2020

Molecular-dynamics simulation methods for macromolecular crystallography

por Wych, David C., Aoto, Phillip C., Vu, Lily, Wolff, Alexander M., Mobley, David L., Fraser, James S., Taylor, Susan S., Wall, Michael E.
Publicado 2023

Evaluation of log P, pK(a), and log D predictions from the SAMPL7 blind challenge

por Bergazin, Teresa Danielle, Tielker, Nicolas, Zhang, Yingying, Mao, Junjun, Gunner, M. R., Francisco, Karol, Ballatore, Carlo, Kast, Stefan M., Mobley, David L.
Publicado 2021

Prioritizing Small Sets of Molecules for Synthesis through in‐silico Tools: A Comparison of Common Ranking Methods

por Breznik, Marko, Ge, Yunhui, Bluck, Joseph P., Briem, Hans, Hahn, David F., Christ, Clara D., Mortier, Jérémie, Mobley, David L., Meier, Katharina
Publicado 2022

Building Block-Based Binding Predictions for DNA-Encoded Libraries

por Zhang, Chris, Pitman, Mary, Dixit, Anjali, Leelananda, Sumudu, Palacci, Henri, Lawler, Meghan, Belyanskaya, Svetlana, Grady, LaShadric, Franklin, Joe, Tilmans, Nicolas, Mobley, David L.
Publicado 2023

An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA

por Nainar, Sarah, Cuthbert, Bonnie, Lim, Nathan M., England, Whitney E., Ke, Ke, Sophal, Kanika, Quechol, Robert, Mobley, David L., Goulding, Celia W., Spitale, Robert C.
Publicado 2020

Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach

por Baumann, Hannah M., Dybeck, Eric, McClendon, Christopher L., Pickard, Frank C., Gapsys, Vytautas, Pérez-Benito, Laura, Hahn, David F., Tresadern, Gary, Mathiowetz, Alan M., Mobley, David L.
Publicado 2023