| Deciphering protein evolution and fitness landscapes with latent space models X Ding, Z Zou, CL Brooks III Nature communications 10 (1), 5644, 2019 | 90 | 2019 |
| Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data Y Wu, B Shi, X Ding, T Liu, X Hu, KY Yip, ZR Yang, DH Mathews, ZJ Lu Nucleic acids research 43 (15), 7247-7259, 2015 | 89 | 2015 |
| Mechanism of Vps4 hexamer function revealed by cryo-EM M Su, EZ Guo, X Ding, Y Li, JT Tarrasch, CL Brooks III, Z Xu, G Skiniotis Science Advances 3 (4), e1700325, 2017 | 61 | 2017 |
| Accelerated CDOCKER with GPUs, parallel simulated annealing, and fast Fourier transforms X Ding, Y Wu, Y Wang, JZ Vilseck, CL Brooks III Journal of chemical theory and computation 16 (6), 3910-3919, 2020 | 44 | 2020 |
| Fast solver for large scale multistate Bennett acceptance ratio equations X Ding, JZ Vilseck, CL Brooks III Journal of chemical theory and computation 15 (2), 799-802, 2019 | 38 | 2019 |
| Gibbs sampler-based λ-dynamics and Rao–Blackwell estimator for alchemical free energy calculation X Ding, JZ Vilseck, RL Hayes, CL Brooks III Journal of chemical theory and computation 13 (6), 2501-2510, 2017 | 37 | 2017 |
| DeepBAR: a fast and exact method for binding free energy computation X Ding, B Zhang The journal of physical chemistry letters 12 (10), 2509-2515, 2021 | 36 | 2021 |
| Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface X Ding, X Lin, B Zhang Nature communications 12 (1), 1091, 2021 | 32 | 2021 |
| Computing absolute free energy with deep generative models X Ding, B Zhang Biophysical Journal 120 (3), 195a, 2021 | 17 | 2021 |
| Contrastive learning of coarse-grained force fields X Ding, B Zhang Journal of chemical theory and computation 18 (10), 6334-6344, 2022 | 16 | 2022 |
| Learning deep generative models with annealed importance sampling X Ding, DJ Freedman arXiv preprint arXiv:1906.04904, 2019 | 13* | 2019 |
| CDOCKER and -dynamics for prospective prediction in D3R Grand Challenge 2 X Ding, RL Hayes, JZ Vilseck, MK Charles, CL Brooks III Journal of computer-aided molecular design 32 (1), 89-102, 2018 | 9 | 2018 |
| Generalizing the discrete Gibbs sampler-based λ-dynamics approach for multisite sampling of many ligands JZ Vilseck, X Ding, RL Hayes, CL Brooks III Journal of chemical theory and computation 17 (7), 3895-3907, 2021 | 8 | 2021 |
| Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction G Schuette, X Ding, B Zhang Biophysical Journal 122 (17), 3425-3438, 2023 | 3 | 2023 |
| Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling MT Robo, RL Hayes, X Ding, B Pulawski, JZ Vilseck Nature Communications 14 (1), 8515, 2023 | 2 | 2023 |
| Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks J Airas, X Ding, B Zhang ACS Central Science 9 (12), 2286-2297, 2023 | 2 | 2023 |
| OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates S Liu, C Wang, AP Latham, X Ding, B Zhang PLoS Computational Biology 19 (9), e1011442, 2023 | 2 | 2023 |
| Achieving Rapid Free Energy Estimates from λ-Dynamics with Bias Updated Gibbs Sampling M Robo, R Hayes, X Ding, B Pulawski, J Vilseck | 1 | 2022 |
| Methodological Advances for Drug Discovery and Protein Engineering X Ding | 1 | 2018 |
| Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting X Ding | | 2024 |
Charles L. Brooks IIICyrus Levinthal Distinguished University Professor of Chemistry and Biophysics; Warner-Lambert/ParkeVerified email at umich.edu
