Galerkin approximation of dynamical quantities using trajectory data EH Thiede, D Giannakis, AR Dinner, J Weare The Journal of Chemical Physics 150 (24), 244111, 2019 | 81 | 2019 |
Autobahn: Automorphism-based graph neural nets E Thiede, W Zhou, R Kondor Advances in Neural Information Processing Systems 34, 29922-29934, 2021 | 50 | 2021 |
Eigenvector method for umbrella sampling enables error analysis EH Thiede, B Van Koten, J Weare, AR Dinner The Journal of Chemical Physics 145 (8), 084115, 2016 | 50 | 2016 |
A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments J Giraldo-Barreto, S Ortiz, EH Thiede, K Palacio-Rodriguez, B Carpenter, ... arXiv preprint arXiv:2102.02077, 2021 | 37 | 2021 |
Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding A Antoszewski, CJ Feng, BP Vani, EH Thiede, L Hong, J Weare, ... The journal of physical chemistry B 124 (27), 5571-5587, 2020 | 36 | 2020 |
Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights L Hong, BP Vani, EH Thiede, MJ Rust, AR Dinner Proceedings of the National Academy of Sciences 115 (49), E11475-E11484, 2018 | 32 | 2018 |
The general theory of permutation equivarant neural networks and higher order graph variational encoders EH Thiede, TS Hy, R Kondor arXiv preprint arXiv:2004.03990, 2020 | 28 | 2020 |
Integrated variational approach to conformational dynamics: A robust strategy for identifying eigenfunctions of dynamical operators C Lorpaiboon, EH Thiede, RJ Webber, J Weare, AR Dinner The Journal of Physical Chemistry B 124 (42), 9354-9364, 2020 | 23 | 2020 |
Stratification as a general variance reduction method for Markov chain Monte Carlo AR Dinner, EH Thiede, B Van Koten, J Weare arXiv preprint arXiv:1705.08445, 2017 | 20 | 2017 |
Sharp entrywise perturbation bounds for Markov chains E Thiede, B Van Koten, J Weare SIAM Journal on Matrix Analysis and Applications 36 (3), 917-941, 2015 | 18 | 2015 |
Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy WS Tang, ED Zhong, SM Hanson, EH Thiede, P Cossio Current Opinion in Structural Biology 81, 102626, 2023 | 15 | 2023 |
A community-powered search of machine learning strategy space to find NMR property prediction models LA Bratholm, W Gerrard, B Anderson, S Bai, S Choi, L Dang, P Hanchar, ... Plos one 16 (7), e0253612, 2021 | 14 | 2021 |
Ensemble reweighting using cryo-EM particle images WS Tang, D Silva-Sánchez, J Giraldo-Barreto, B Carpenter, SM Hanson, ... The Journal of Physical Chemistry B 127 (24), 5410-5421, 2023 | 13 | 2023 |
Error bounds for dynamical spectral estimation RJ Webber, EH Thiede, D Dow, AR Dinner, J Weare SIAM journal on mathematics of data science 3 (1), 225-252, 2021 | 9 | 2021 |
Protein dynamics underlying allosteric regulation MA Astore, AS Pradhan, EH Thiede, SM Hanson Current Opinion in Structural Biology 84, 102768, 2024 | 4 | 2024 |
Group-equivariant neural networks with fusion diagrams Z Li, H Zheng, E Thiede, J Liu, R Kondor arXiv preprint arXiv:2211.07482 88, 2022 | 4 | 2022 |
Understanding the sources of error in MBAR through asymptotic analysis XS Li, B Van Koten, AR Dinner, EH Thiede The Journal of Chemical Physics 158 (21), 2023 | 2 | 2023 |
Graph neural networks for biochemistry that incorporate substructure EH Thiede, W Zhou, R Kondor Biophysical Journal 121 (3), 531a, 2022 | 2 | 2022 |
Unifying O (3) equivariant neural networks design with tensor-network formalism Z Li, Z Pengmei, H Zheng, E Thiede, J Liu, R Kondor Machine Learning: Science and Technology 5 (2), 025044, 2024 | 1 | 2024 |
Uncovering the protein structural ensemble by integrating molecular modeling with cryo-EM D Silva-Sánchez, J Moomaw, WS Tang, SM Hanson, R Lederman, ... Biophysical Journal 123 (3), 183a-184a, 2024 | | 2024 |