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.
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Journal ArticleDOI
A Geodesic Framework for Analyzing Molecular Similarities
TL;DR: A procedure for determining the neighborhood radius by examining the tradeoff between the stress function and the number of connected components in the neighborhood graph is described and it is shown that it can be used to produce meaningful maps in any embedding dimension.
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Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage
Huafeng Xu,Aaron G. Schmidt,Timothy O'Donnell,Matthew D. Therkelsen,Thomas B. Kepler,M. Anthony Moody,Barton F. Haynes,Hua-Xin Liao,Stephen C. Harrison,David E. Shaw +9 more
TL;DR: The results support models of the germinal center reaction in which two or more mutations can occur without concomitant selection and show how divergent pathways have yielded functionally equivalent antibodies.
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Multicanonical jump walk annealing: An efficient method for geometric optimization
Huafeng Xu,Bruce J. Berne +1 more
TL;DR: In this article, a new global optimization method, multicanonical jump walk annealing (MJWA), is proposed and applied to the geometric optimization of Lennard-Jones and Morse clusters and the hydrophobic (B), hydrophilic (L), and neutral (N) (BLN) protein model.
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Stochastic Proximity Embedding: Methods and Applications
TL;DR: Some of the key applications of the stochastic proximity embedding algorithm are reviewed, known limitations and ways to circumvent them are outlined, and additional problem domains where the use of this technique could lead to significant breakthroughs are highlighted.
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Computationally efficient molecular dynamics integrators with improved sampling accuracy
Cristian Predescu,Ross A. Lippert,Michael P. Eastwood,Douglas J. Ierardi,Huafeng Xu,Morten Ø. Jensen,Kevin J. Bowers,Justin Gullingsrud,C. A. Rendleman,Ron O. Dror,David E. Shaw +10 more
TL;DR: This work introduces a class of explicit variational integrators designed to achieve high accuracy for quadratic potentials, with little additional computation relative to traditional integrators, and shows that they improve accuracy for classical biomolecular simulations.