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Author Details

Xinqiang Ding
Massachusetts Institute of Technology
2015
16
9
PMIDPaper TitleJournal TitlePublished Year
37131742OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates.bioRxiv2023
37745447Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks.bioRxiv2023
37695778OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.PLoS Comput Biol2023
37496267Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophys J2023
36112935Contrastive Learning of Coarse-Grained Force Fields.J Chem Theory Comput2022
34101448Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands.J Chem Theory Comput2021
33719449DeepBAR: A Fast and Exact Method for Binding Free Energy Computation.J Phys Chem Lett2021
33597548Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nat Commun2021
32374996Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms.J Chem Theory Comput2020
33143418Computing Absolute Free Energy with Deep Generative Models.J Phys Chem B2020
30689377Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.J Chem Theory Comput2019
31822668Deciphering protein evolution and fitness landscapes with latent space models.Nat Commun2019
28884249CDOCKER and λ-dynamics for prospective prediction in D⿿R Grand Challenge 2.J Comput Aided Mol Des2018
28510433Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.J Chem Theory Comput2017
28439563Mechanism of Vps4 hexamer function revealed by cryo-EM.Sci Adv2017
26170232Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.Nucleic Acids Res2015
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Collaborators

Charles L Brooks
University of Michigan ann arbor
Co-authored papers 7
Bin Zhang
Massachusetts Institute of Technology
Co-authored papers 4
Andrew P Latham
Massachusetts Institute of Technology, University of California, San Francisco, University of Notre Dame
Co-authored papers 2
Georgios Skiniotis
Stanford University School of Medicine
Co-authored papers 1
Cong Wang
Massachusetts Institute of Technology
Co-authored papers 1
Bin Zhang
Massachusetts Institute of Technology
Co-authored papers 1
Shuming Liu
Massachusetts Institute of Technology
Co-authored papers 1
Xingcheng Lin
Massachusetts Institute of Technology
Co-authored papers 1
Kevin Y Yip
Co-authored papers 1
Release 1.2