Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution

por Wieder, Marcus, Fass, Josh, Chodera, John D.
Publicado 2021

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

por Sivak, David A., Chodera, John D., Crooks, Gavin E.
Publicado 2014

Benchmarking Cross-Docking Strategies for Structure-Informed Machine Learning in Kinase Drug Discovery

por Schaller, David, Christ, Clara D., Chodera, John D., Volkamer, Andrea
Publicado 2023

Is structure based drug design ready for selectivity optimization?

por Albanese, Steven K., Chodera, John D., Volkamer, Andrea, Keng, Simon, Abel, Robert, Wang, Lingle
Publicado 2020

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

por Parton, Daniel L., Grinaway, Patrick B., Hanson, Sonya M., Beauchamp, Kyle A., Chodera, John D.
Publicado 2016

OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes

por Swenson, David W. H., Prinz, Jan-Hendrik, Noe, Frank, Chodera, John D., Bolhuis, Peter G.
Publicado 2018

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics

por Swenson, David W. H., Prinz, Jan-Hendrik, Noe, Frank, Chodera, John D., Bolhuis, Peter G.
Publicado 2018

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems

por Fass, Josh, Sivak, David A., Crooks, Gavin E., Beauchamp, Kyle A., Leimkuhler, Benedict, Chodera, John D.
Publicado 2018

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

por Hauser, Kevin, Negron, Christopher, Albanese, Steven K., Ray, Soumya, Steinbrecher, Thomas, Abel, Robert, Chodera, John D., Wang, Lingle
Publicado 2018

Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex

por Zhang, Ivy, Rufa, Dominic A., Pulido, Iván, Henry, Michael M., Rosen, Laura E., Hauser, Kevin, Singh, Sukrit, Chodera, John D.
Publicado 2023

Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model

por Morris, Aaron, McCorkindale, William, Consortium, The COVID Moonshot, Drayman, Nir, Chodera, John D., Tay, Savaş, London, Nir, Lee, Alpha A.
Publicado 2021

Ancestral reconstruction reveals mechanisms of ERK regulatory evolution

por Sang, Dajun, Pinglay, Sudarshan, Wiewiora, Rafal P, Selvan, Myvizhi E, Lou, Hua Jane, Chodera, John D, Turk, Benjamin E, Gümüş, Zeynep H, Holt, Liam J
Publicado 2019

Turning high-throughput structural biology into predictive inhibitor design

por Saar, Kadi L., McCorkindale, William, Fearon, Daren, Boby, Melissa, Barr, Haim, Ben-Shmuel, Amir, London, Nir, von Delft, Frank, Chodera, John D., Lee, Alpha A.
Publicado 2023

End-to-end differentiable construction of molecular mechanics force fields

por Wang, Yuanqing, Fass, Josh, Kaminow, Benjamin, Herr, John E., Rufa, Dominic, Zhang, Ivy, Pulido, Iván, Henry, Mike, Bruce Macdonald, Hannah E., Takaba, Kenichiro, Chodera, John D.
Publicado 2022

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

por Nguyen, Trung Hai, Rustenburg, Ariën S., Krimmer, Stefan G., Zhang, Hexi, Clark, John D., Novick, Paul A., Branson, Kim, Pande, Vijay S., Chodera, John D., Minh, David D. L.
Publicado 2018

L-2-hydroxyglutarate production arises from non-canonical enzyme function at acidic pH

por Intlekofer, Andrew M., Wang, Bo, Liu, Hui, Shah, Hardik, Carmona-Fontaine, Carlos, Rustenburg, Ariën S., Salah, Salah, Gunner, M. R., Chodera, John D., Cross, Justin R., Thompson, Craig B.
Publicado 2017

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

por Eastman, Peter, Behara, Pavan Kumar, Dotson, David L., Galvelis, Raimondas, Herr, John E., Horton, Josh T., Mao, Yuezhi, Chodera, John D., Pritchard, Benjamin P., Wang, Yuanqing, De Fabritiis, Gianni, Markland, Thomas E.
Publicado 2023

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation

por Ruff, Emily F, Muretta, Joseph M, Thompson, Andrew R, Lake, Eric W, Cyphers, Soreen, Albanese, Steven K, Hanson, Sonya M, Behr, Julie M, Thomas, David D, Chodera, John D, Levinson, Nicholas M
Publicado 2018

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

por Horton, Joshua T., Boothroyd, Simon, Wagner, Jeffrey, Mitchell, Joshua A., Gokey, Trevor, Dotson, David L., Behara, Pavan Kumar, Ramaswamy, Venkata Krishnan, Mackey, Mark, Chodera, John D., Anwar, Jamshed, Mobley, David L., Cole, Daniel J.
Publicado 2022

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

por Eastman, Peter, Swails, Jason, Chodera, John D., McGibbon, Robert T., Zhao, Yutong, Beauchamp, Kyle A., Wang, Lee-Ping, Simmonett, Andrew C., Harrigan, Matthew P., Stern, Chaya D., Wiewiora, Rafal P., Brooks, Bernard R., Pande, Vijay S.
Publicado 2017