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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Proceedings ArticleDOI
Scalable algorithms for molecular dynamics simulations on commodity clusters
Kevin J. Bowers,Edmond Chow,Huafeng Xu,Ron O. Dror,Michael P. Eastwood,Brent A. Gregersen,John L. Klepeis,István Kolossváry,Mark A. Moraes,Federico D. Sacerdoti,John K. Salmon,Yibing Shan,David E. Shaw +12 more
TL;DR: This work presents several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes, including a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time.
Journal ArticleDOI
Biomolecular Simulation: A Computational Microscope for Molecular Biology
TL;DR: The rapidly evolving state of the art for atomic-level biomolecular simulation is described, the types of biological discoveries that can now be made through simulation are illustrated, and challenges motivating continued innovation in this field are discussed.
Journal ArticleDOI
Pathway and mechanism of drug binding to G-protein-coupled receptors
Ron O. Dror,Albert C. Pan,Daniel H. Arlow,David W. Borhani,Paul Maragakis,Yibing Shan,Huafeng Xu,David E. Shaw,David E. Shaw +8 more
TL;DR: An atomic-level description of the binding process suggests opportunities for allosteric modulation and provides a structural foundation for future optimization of drug–receptor binding and unbinding rates.
Journal ArticleDOI
Activation mechanism of the β2-adrenergic receptor
Ron O. Dror,Daniel H. Arlow,Paul Maragakis,Thomas J. Mildorf,Albert C. Pan,Huafeng Xu,David W. Borhani,David E. Shaw +7 more
TL;DR: An activation mechanism for the β2-adrenergic receptor, a prototypical GPCR, is proposed based on atomic-level simulations in which an agonist-bound receptor transitions spontaneously from the active to the inactive crystallographically observed conformation.
Journal ArticleDOI
A conserved protonation-dependent switch controls drug binding in the Abl kinase
Yibing Shan,Markus A. Seeliger,Michael P. Eastwood,Filipp Frank,Huafeng Xu,Morten Ø. Jensen,Ron O. Dror,John Kuriyan,David E. Shaw +8 more
TL;DR: This model suggests a possible explanation for the high degree of conservation of the DFG motif: that the flip, modulated by electrostatic changes inherent to the catalytic cycle, allows the kinase to access flexible conformations facilitating nucleotide binding and release.