Chodera, John D.

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

Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology

Parallel Computing and Optimization TechniquesProtein Structure and Dynamics

Cited by 2,748

Current Status of the AMOEBA Polarizable Force Field

Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., et al. (2010) · The Journal of Physical Chemistry B

Advanced Chemical Physics StudiesAdvanced Physical and Chemical Molecular Interactions

Cited by 1,440

Markov models of molecular kinetics: Generation and validation

Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne, M., Held, M., Chodera, J. D., Schütte, C., & Noé, F. (2011) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 1,275

Markov state models of biomolecular conformational dynamics

Chodera, J. D., & Noé, F. (2014) · Current Opinion in Structural Biology

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 776

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell

SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approaches

Cited by 606

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Chodera, J. D., & Mobley, D. L. (2013) · Annual Review of Biophysics

thermodynamics and calorimetric analysesProtein Interaction Studies and Fluorescence Analysis

Cited by 531

Hypoxia Induces Production of L-2-Hydroxyglutarate

Intlekofer, A. M., Dematteo, R. G., Venneti, S., Finley, L. W. S., Lu, C., Judkins, A. R., Rustenburg, A. S., Grinaway, P. B., Chodera, J. D., Cross, J. R., et al. (2015) · Cell Metabolism

Cancer, Hypoxia, and MetabolismEpigenetics and DNA Methylation

Cited by 513

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Mobley, D. L., Chodera, J. D., & Dill, K. A. (2006) · The Journal of Chemical Physics

Computational Drug Discovery MethodsAdvanced Physical and Chemical Molecular Interactions

Cited by 316

Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

Mobley, D. L., Graves, A. P., Chodera, J. D., McReynolds, A. C., Shoichet, B. K., & Dill, K. A. (2007) · Journal of Molecular Biology

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 310

Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations

Intlekofer, A. M., Shih, A. H., Wang, B., Nazir, A., Rustenburg, A. S., Albanese, S. K., Patel, M., Famulare, C., Correa, F. M., Takemoto, N., et al. (2018) · Nature

Acute Myeloid Leukemia ResearchGlioma Diagnosis and Treatment

Cited by 281

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH

Intlekofer, A. M., Wang, B., Liu, H., Shah, H., Carmona-Fontaine, C., Rustenburg, A. S., Salah, S., Gunner, M. R., Chodera, J. D., Cross, J. R., et al. (2017) · Nature Chemical Biology

Cancer, Hypoxia, and MetabolismBiochemical Acid Research Studies

Cited by 268

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

Noé, F., Doose, S., Daidone, I., Löllmann, M., Sauer, M., Chodera, J. D., & Smith, J. C. (2011) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsAdvanced Fluorescence Microscopy Techniques

Cited by 116

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Ackloo, S., Al-awar, R., Amaro, R. E., Arrowsmith, C. H., Azevedo, H., Batey, R. A., Bengio, Y., Betz, U. A. K., Bologa, C. G., Chodera, J. D., et al. (2022) · Nature Reviews Chemistry

Computational Drug Discovery MethodsProtein Degradation and Inhibitors

Cited by 112

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

Chodera, J. D., Swope, W. C., Noé, F., Prinz, J.-H., Shirts, M. R., & Pande, V. S. (2011) · The Journal of Chemical Physics

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 71

What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models

Suárez, E., Wiewiora, R. P., Wehmeyer, C., Noé, F., Chodera, J. D., & Zuckerman, D. M. (2020) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 65

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

Suárez, E., Wiewiora, R. P., Wehmeyer, C., Noé, F., Chodera, J. D., & Zuckerman, D. M. (2021) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 65

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Prinz, J.-H., Chodera, J. D., Pande, V. S., Swope, W. C., Smith, J. C., & Noé, F. (2011) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 52

Trastuzumab Deruxtecan Resistance via Loss of HER2 Expression and Binding

Chen, W., Gupta, A., Mai, N., Nag, S., Lau, J. S., Singh, S., Chodera, J. D., Liu, B., de Stanchina, E., Pareja, F., et al. (2026) · Cancer Discovery

HER2/EGFR in Cancer ResearchLung Cancer Treatments and Mutations

Cited by 50

Spectral rate theory for two-state kinetics

Prinz, J.-H., Chodera, J. D., & Noé, F. (2014) · Physical Review X

Advanced Fluorescence Microscopy TechniquesAdvanced Physical and Chemical Molecular Interactions

Cited by 21