Morten Ø. Jensen, David W. Borhani, Kresten Lindorff-Larsen, Paul Maragakis, Vishwanath Jogini, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Principles of Conduction and Hydrophobic Gating in K+ Channels," Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 13, 2010, pp. 5833–5838. Text
Ron O. Dror, Morten Ø. Jensen, David W. Borhani, and David E. Shaw, "Exploring Atomic Resolution Physiology on a Femtosecond to Millisecond Timescale Using Molecular Dynamics Simulations," The Journal of General Physiology, vol. 135, no. 6, 2010, pp. 555–562. Text
Michael P. Eastwood, Kate A. Stafford, Ross A. Lippert, Morten Ø. Jensen, Paul Maragakis, Cristian Predescu, Ron O. Dror, and David E. Shaw, "Equipartition and the Calculation of Temperature in Biomolecular Simulations," Journal of Chemical Theory and Computation, vol. 6, no. 7, 2010, pp. 2045–2058. Text
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw, "Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field," Proteins: Structure, Function, and Bioinformatics, vol. 78, no. 8, 2010, pp. 1950–1958. Text
Tiankai Tu, Charles A. Rendleman, Patrick J. Miller, Federico Sacerdoti, Ron O. Dror, and David E. Shaw, "Accelerating Parallel Analysis of Scientific Simulation Data via Zazen," Proceedings of the 8th USENIX Conference on File and Storage Technologies (FAST '10), San Jose, California, February 23–26, 2010. Text
Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw, "Improved Twiddle Access for Fast Fourier Transforms," IEEE Transactions on Signal Processing, vol. 58, no. 3, 2010, pp. 1122–1130. Text
David E. Shaw, Ron O. Dror, John K. Salmon, J.P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles, "Millisecond-Scale Molecular Dynamics Simulations on Anton," Proceedings of the ACM/IEEE Conference on Supercomputing (SC09), Portland, Oregon, November 14–20, 2009. Text
Gordon Bell Prize; Best Paper Award.
Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, and David E. Shaw, "Identification of Two Distinct Inactive Conformations of the ß2-Adrenergic Receptor Reconciles Structural and Biochemical Observations," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 12, 2009, pp. 4689–4694. Text
Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, Filipp Frank, Huafeng Xu, Morten Ø. Jensen, Ron O. Dror, John Kuriyan, and David E. Shaw, "A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 1, 2009, pp. 139–144. Text
Daniel K. Shenfeld, Huafeng Xu, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Minimizing Thermodynamic Length to Select Intermediate States for Free-Energy Calculations and Replica-Exchange Simulations," Physical Review E, vol. 80, no. 4, 2009, pp. 046705-1–046705-4. Text
Markus A. Seeliger, Pratistha Ranjitkar, Corynn Kasap, Yibing Shan, David E. Shaw, Neil P. Shah, John Kuriyan, and Dustin J. Maly, "Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations," Cancer Research, vol. 69, no. 6, 2009, pp. 2384–2392. Text
Cliff Young, Joseph A. Bank, Ron O. Dror, J.P. Grossman, John K. Salmon, and David E. Shaw, "A 32×32×32, Spatially Distributed 3D FFT in Four Microseconds on Anton," Proceedings of the ACM/IEEE Conference on Supercomputing (SC09), Portland, Oregon, November 14–20, 2009. Text
C. Richard Ho, Michael Theobald, Brannon Batson, J.P. Grossman, Stanley C. Wang, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, "Post-Silicon Debug Using Formal Verification Waypoints," Proceedings of the Design and Verification Conference and Exhibition (DVCon '09), San Jose, California, February 24–26, 2009. Text
John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, and David E. Shaw, "Long-Timescale Molecular Dynamics Simulations of Protein Structure and Function," Current Opinion in Structural Biology, vol. 19, 2009, pp. 1–18. Text
Willy Wriggers, Kate A. Stafford, Yibing Shan, Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations," Journal of Chemical Theory and Computation, vol. 5, no. 10, 2009, pp. 2595–2605. Text
Morten Ø. Jensen, Ron O. Dror, Huafeng Xu, David W. Borhani, Isaiah T. Arkin, Michael P. Eastwood, and David E. Shaw, "Dynamic Control of Slow Water Transport by Aquaporin 0: Implications for Hydration and Junction Stability in the Eye Lens," Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 38, 2008, pp. 14430–14435. Text
Paul Maragakis, Kresten Lindorff-Larsen, Michael P. Eastwood, Ron O. Dror, John L. Klepeis, Isaiah T. Arkin, Morten Ø. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arthur G. Palmer III, and David E. Shaw, "Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins," Journal of Physical Chemistry B, vol. 112, no. 19, 2008, pp. 6155–6158. Text
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J.P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, and Stanley C. Wang, "Anton, A Special-Purpose Machine for Molecular Dynamics Simulation," Communications of the ACM, vol. 51, no. 7, 2008, pp. 91–97. Text
Tiankai Tu, Charles A. Rendleman, David W. Borhani, Ron O. Dror, Justin
Gullingsrud, Morten Ø. Jensen, John L. Klepeis, Paul Maragakis, Patrick
Miller, Kate A. Stafford, and David E. Shaw, "A Scalable Parallel Framework for
Analyzing Terascale Molecular Dynamics Simulation Trajectories," Proceedings
of the ACM/IEEE Conference on Supercomputing (SC08), Austin, Texas,
November 15–21, 2008. Text
Best Paper Award Finalist.
Jeffrey S. Kuskin, Cliff Young, J.P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, "Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation," Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), Salt Lake City, Utah, February 16–20, 2008. Text
Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J.P. Grossman, Yibing Shan, John L. Klepeis, and David E. Shaw, "High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation," Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), Salt Lake City, Utah, February 16–20, 2008. Text
J.P. Grossman, John K. Salmon, C. Richard Ho, Douglas J. Ierardi, Brian Towles, Brannon Batson, Jochen Spengler, Stanley C. Wang, Rolf Mueller, Michael Theobald, Cliff Young, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, "Hierarchical Simulation-Based Verification of Anton, a Special-Purpose Parallel Machine," Proceedings of the 26th IEEE International Conference on Computer Design (ICCD '08), Lake Tahoe, California, October 12–15, 2008. Text
C. Richard Ho, Michael Theobald, Martin M. Deneroff, Ron O. Dror, Joseph Gagliardo, and David E. Shaw, "Early Formal Verification of Conditional Coverage Points to Identify Intrinsically Hard-to-Verify Logic," Proceedings of the 45th Annual Design Automation Conference (DAC '08), Anaheim, California, June 9–13, 2008. Text
J.P. Grossman, Cliff Young, Joseph A. Bank, Kenneth Mackenzie, Douglas J. Ierardi, John K. Salmon, Ron O. Dror, and David E. Shaw, "Simulation and Embedded Software Development for Anton, a Parallel Machine with Heterogeneous Multicore ASICs," Proceedings of the 6th IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES/ISSS '08), Atlanta, Georgia, October 19–24, 2008. Text
Isaiah T. Arkin, Huafeng Xu, Morten Ø. Jensen, Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman-Tene, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Yibing Shan, and David E. Shaw, "Mechanism of Na+/H+ Antiporting," Science, vol. 317, no. 5839, 2007, pp. 799–803. Text
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J.P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, and Stanley C. Wang, "Anton: A Special-Purpose Machine for Molecular Dynamics Simulation," Proceedings of the 34th Annual International Symposium on Computer Architecture (ISCA '07), San Diego, California, June 9–13, 2007. Text
Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, and David E. Shaw, "A Common, Avoidable Source of Error in Molecular Dynamics Integrators," Journal of Chemical Physics, vol. 126, no. 4, 2007, pp. 046101:1–2. Text
Kevin J. Bowers, Ron O. Dror, and David E. Shaw, "Zonal Methods for the Parallel Execution of Range-Limited N-Body Simulations," Journal of Computational Physics, vol. 221, no. 1, 2007, pp. 303–329. Text
Kevin J. Bowers, Ron O. Dror, and David E. Shaw, "The Midpoint Method for Parallelization of Particle Simulations," Journal of Chemical Physics, vol. 124, no. 18, 2006, pp. 184109:1–11. Text
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, and David E. Shaw,
"Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,"
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa,
Florida, November 11–17, 2006. Text
Best Paper Award.
David E. Shaw, "A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions," Journal of Computational Chemistry, vol. 26, no. 13, 2005, pp. 1318–1328. Text
Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw, "Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation," Journal of Chemical Physics, vol. 122, no. 5, 2005, pp. 054101:1–13. Text
Edmond Chow, Charles A. Rendleman, Kevin J. Bowers, Ron O. Dror, Douglas H. Hughes, Justin Gullingsrud, Federico D. Sacerdoti, and David E. Shaw, "Desmond Performance on a Cluster of Multicore Processors," D. E. Shaw Research Technical Report DESRES/TR--2008-01, July 2008. Text