Publications

Qiu et al., Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design, JACS Au, 4, 3857-3868, 2024.

Jones et al., Molecular latent space simulators for distributed and multimolecular trajectories, Journal of Physical Chemistry A, 127, 5470-5490, 2023.

Mostofian et al., Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods, Journal of Chemical Information and Modeling, 63, 5408-5432, 2023.

Dixon et al., Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry, Nature Communications, 13, 1-24, 2022.

Xu et al., Characterizing receptor flexibility to predict mutations that lead to human adaptation of influenza hemagglutinin, Journal of Chemical Theory and Computation, 18, 4995-5005, 2022.

Huafeng Xu, Molecular simulations minimally restrained by experimental data, Journal of Chemical Physics, 150, 154121, 2019.

Park et al., Modeling the effect of cooperativity in ternary complex formation and targeted protein degradation mediated by heterobifunctional degraders, ACS Bio Med Chem Au, 3, 74-86, 2023.

Huafeng Xu, ATP-driven Non-equilibrium Activation of Kinase Clients by the Molecular Chaperone Hsp90, Biophysical Journal, 119, 1538-1549, 2020.

Huafeng Xu, Cochaperones enable Hsp70 to use ATP energy to stabilize native proteins out of the folding equilibrium, Scientific Report, 8, 13213, 2018.

Huafeng Xu, The slow but steady rise of binding free energy calculations in drug discovery, Journal of Computer-Aided Molecular Design, 37, 67-74, 2022.

Li et al., Precise binding free energy calculations for multiple molecules using an optimal measurement network of pairwise differences, Journal of Chemical Theory and Computation, 18, 650-663, 2021.

Huafeng Xu, Optimal measurement network of pairwise differences, Journal of Chemical Information and Modeling, 59, 4720-4728, 2019.

Lieyang Chen et al., Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands, Journal of Chemical Information and Modeling, 64, 250-264, 2024.

Sheenam Khuttan et al., Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host–guest SAMPL9 blinded challenge, Physical Chemistry Chemical Physics, 25, 24364-24367, 2023.