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2020 – today
- 2020
[j17]Mehtap Isik
, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley:
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J. Comput. Aided Mol. Des. 34(4): 335-370 (2020)- [j16]Mehtap Isik, Dorothy Levorse, David L. Mobley, Timothy Rhodes, John D. Chodera:
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J. Comput. Aided Mol. Des. 34(4): 405-420 (2020) - [j15]Marilyn R. Gunner, Taichi Murakami, Ariën S. Rustenburg, Mehtap Isik, John D. Chodera:
Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states. J. Comput. Aided Mol. Des. 34(5): 561-573 (2020) - [j14]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:
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 34(5): 601-633 (2020) - [j13]Steven K. Albanese, John D. Chodera, Andrea Volkamer, Simon Keng, Robert Abel, Lingle Wang:
Is Structure-Based Drug Design Ready for Selectivity Optimization? J. Chem. Inf. Model. 60(12): 6211-6227 (2020) - [i2]Yuanqing Wang, Josh Fass, John D. Chodera:
End-to-End Differentiable Molecular Mechanics Force Field Construction. CoRR abs/2010.01196 (2020)
2010 – 2019
- 2019
- [j12]Mark James Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M. J. J. Bonvin, Matthieu Chavent, John D. Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikael Trellet, Christopher J. Woods, Artem A. Zhmurov:
Sharing Data from Molecular Simulations. J. Chem. Inf. Model. 59(10): 4093-4099 (2019) - [i1]Yuanqing Wang, Josh Fass, Chaya D. Stern, Kun Luo, John D. Chodera:
Graph Nets for Partial Charge Prediction. CoRR abs/1909.07903 (2019) - 2018
- [j11]Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle Beauchamp, Benedict J. Leimkuhler, John D. Chodera:
Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. Entropy 20(5): 318 (2018) - [j10]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:
Overview of the SAMPL6 host-guest binding affinity prediction challenge. J. Comput. Aided Mol. Des. 32(10): 937-963 (2018) - [j9]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:
pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J. Comput. Aided Mol. Des. 32(10): 1117-1138 (2018) - 2017
- [j8]Peter Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande:
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. 13(7) (2017) - 2016
- [j7]Ariën S. Rustenburg, Justin Dancer, Baiwei Lin, Jianwen A. Feng, Daniel F. Ortwine, David L. Mobley, John D. Chodera:
Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. J. Comput. Aided Mol. Des. 30(11): 945-958 (2016) - [j6]Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle Beauchamp, John D. Chodera:
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. PLoS Comput. Biol. 12(6) (2016) - 2015
- [j5]Christian Kramer, John D. Chodera, Terry R. Stouch:
Introduction to the special issue: Data Part 2: Experimental Data. J. Comput. Aided Mol. Des. 29(9): 777 (2015) - [j4]Sonya M. Hanson, Sean Ekins, John D. Chodera:
Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. J. Comput. Aided Mol. Des. 29(12): 1073-1086 (2015) - 2013
- [j3]Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts:
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J. Comput. Aided Mol. Des. 27(12): 989-1007 (2013)
2000 – 2009
- 2006
- [j2]John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill:
Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations. Multiscale Model. Simul. 5(4): 1214-1226 (2006) - 2003
- [j1]Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill:
MOPED: Method for optimizing physical energy parameters using decoys. J. Comput. Chem. 24(1): 89-97 (2003)
Coauthor Index
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