Research

D. E. Shaw Research has always been a research‑driven organization. Many of the computational methods and scientific discoveries we now make use of on a daily basis are the product of improbably ambitious goals and unabashedly speculative ideas that we mapped out some years ago. This approach has served us well, and we continue to engage in highly ambitious, often speculative research whose potential payoffs are targeted some years in the future.

Our work encompasses an unusually wide range of activities, from the design of new supercomputers to the design of new drug molecules. The breadth of these activities is reflected in the breadth of the research that drives them, which includes investigations involving various aspects of

  • Parallel computer architectures
    • Special‑purpose integrated circuit design
    • Massively parallel on‑chip arithmetic hardware
    • High‑bandwidth, low‑latency interconnection schemes
    • Specialized high‑performance scientific software
    • Application‑specific design verification
    • System software for massively parallel supercomputing
  • Computational chemistry methods
    • Numerical methods for simulation and analysis
    • Physical models and approximations
    • Conformational sampling methods
    • Estimation of thermodynamic quantities
    • Quantum chemical calculations
    • Various applications of machine learning
  • Atomic‑level mechanisms underlying biological processes
    • Structural changes in proteins and nucleic acids
    • Dynamics of protein⁠–⁠ligand binding
    • Protein⁠–⁠protein interactions
    • Molecular underpinnings of disease
    • Discovery of structural states and binding sites
    • Atomic‑level mechanisms of new and existing drugs

The results of our research have had a significant impact not only at D. E. Shaw Research itself, but within the broader scientific community. In 2010, for example, we published a paper1 in the journal Science describing our use of Anton‑based MD simulations of unprecedented length to provide answers to several longstanding questions regarding the structural dynamics of proteins and the process of protein folding. The findings we reported were named by the journal as one of the 10 most significant scientific breakthroughs of the year,2 and the paper quickly gained considerable attention within the research community, becoming the most‑cited publication in the field of chemistry during the months of July and August 2011.3

  1. Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic‑level characterization of the structural dynamics of proteins. Science  330: 341–346 (2010).
  2. Breakthrough of the Year. Science  330: 1604–1607 (2010).
  3. Thomson Reuters Science Watch  (2011).