H
Huafeng Xu
Researcher at D. E. Shaw Research
Publications - 52
Citations - 6862
Huafeng Xu is an academic researcher from D. E. Shaw Research. The author has contributed to research in topics: Molecular dynamics & Chemistry. The author has an hindex of 27, co-authored 45 publications receiving 5545 citations. Previous affiliations of Huafeng Xu include University of California, San Francisco & Columbia University.
Papers
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Journal ArticleDOI
Best Practices for Alchemical Free Energy Calculations [Article v1.0].
Antonia S. J. S. Mey,Bryce K. Allen,Hannah E. Bruce Macdonald,John D. Chodera,David F. Hahn,Maximilian Kuhn,Julien Michel,David L. Mobley,Levi N. Naden,Samarjeet Prasad,Andrea Rizzi,Jenke Scheen,Michael R. Shirts,Gary Tresadern,Huafeng Xu +14 more
TL;DR: In this paper, the authors review current best practices for several popular application domains of alchemical free energy calculations performed with equilibrium simulations, in particular relative and absolute small molecule binding energy calculations to biomolecular targets.
Journal ArticleDOI
Best Practices for Alchemical Free Energy Calculations
Antonia S. J. S. Mey,Bryce K. Allen,Hannah E. Bruce Macdonald,John D. Chodera,Maximilian Kuhn,Julien Michel,David L. Mobley,Levi N. Naden,Samarjeet Prasad,Andrea Rizzi,Jenke Scheen,Michael R. Shirts,Gary Tresadern,Huafeng Xu +13 more
TL;DR: Current best practices for several popular application domains of alchemical free energy calculations, including relative and absolute small molecule binding free energy Calculations to biomolecular targets are reviewed.
Journal ArticleDOI
Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens
Morten Ø. Jensen,Ron O. Dror,Huafeng Xu,David W. Borhani,Isaiah T. Arkin,Michael P. Eastwood,David E. Shaw +6 more
TL;DR: It is hypothesized that the structural features leading to low permeability may have evolved in part to allow AQP0 to form junctions that both conduct water and contribute to the organizational structure of the fiber cell tissue and microcirculation within it, as required to maintain transparency of the lens.
Journal ArticleDOI
Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations.
TL;DR: This work derives bounds for quantities in terms of the thermodynamic distance between the intermediates in two cases where the choice of intermediate states is particularly important: minimizing statistical error in free-energy difference calculations and maximizing average acceptance probabilities in replica-exchange simulations.
Journal ArticleDOI
A Simple Model of Multivalent Adhesion and Its Application to Influenza Infection.
TL;DR: The model predicts that hemagglutinin inhibitors of relatively modest affinity can dramatically reduce influenza virus adhesion to host cells, suggesting that such inhibitors, if discovered, may be viable therapeutic agents against influenza.