Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, and David E. Shaw, "How Fast-Folding Proteins Fold," Science, vol. 334, no. 6055, 2011, pp. 517–520. Text
John K. Salmon, Mark A. Moraes, Ron O. Dror, and David E. Shaw, "Parallel Random Numbers: As Easy as 1, 2, 3," Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC11), New York, NY: ACM, 2011. Text
Best Paper Award.
Ron O. Dror, Daniel H. Arlow, Paul Maragakis, Thomas J. Mildorf, Albert C. Pan, Huafeng Xu, David W. Borhani, and David E. Shaw, "Activation Mechanism of the β2-Adrenergic Receptor," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 46, 2011, pp. 18684–18689. Text
Ron O. Dror, Albert C. Pan, Daniel H. Arlow, David W. Borhani, Paul Maragakis, Yibing Shan, Huafeng Xu, and David E. Shaw, "Pathway and Mechanism of Drug Binding to G Protein–Coupled Receptors," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 32, 2011, pp. 13118–13123. Text
Yibing Shan, Eric T. Kim, Michael P. Eastwood, Ron O. Dror, Markus A. Seeliger, and David E. Shaw, "How Does a Drug Molecule Find Its Target Binding Site?" Journal of the American Chemical Society, vol. 133, no. 24, 2011, pp. 9181–9183. Text
Stefano Piana, Kresten Lindorff-Larsen, and David E. Shaw, "How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?" Biophysical Journal, vol. 100, no. 9, 2011, pp. L47–L49. Text
J. Adam Butts, Ping Tak Peter Tang, Ron O. Dror, and David E. Shaw, "Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots," Proceedings of the 20th IEEE Symposium on Computer Arithmetic 2011 (ARITH20), Tübingen, Germany: IEEE Computer Society, 2011. In press.
Ping Tak Peter Tang, J. Adam Butts, Ron O. Dror, and David E. Shaw, "Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/√x Design," Proceedings of the 20th IEEE Symposium on Computer Arithmetic 2011 (ARITH20), Tübingen, Germany: IEEE Computer Society, 2011. In press.
Ron O. Dror, J.P. Grossman, Kenneth M. Mackenzie, Brian Towles, Edmond Chow, John K. Salmon, Cliff Young, Joseph A. Bank, Brannon Batson, Martin M. Deneroff, Jeffrey S. Kuskin, Richard H. Larson, Mark A. Moraes, and David E. Shaw, "Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation," IEEE Micro, vol. 31, no. 3, 2011, pp. 8–19. Text
Daniel M. Rosenbaum, Cheng Zhang, Joseph A. Lyons, Ralph Holl, David Aragao, Daniel H. Arlow, Søren G. F. Rasmussen, Hee-Jung Choi, Brian T. DeVree, Roger K. Sunahara, Pil Seok Chae, Samuel H. Gellman, Ron O. Dror, David E. Shaw, William I. Weis, Martin Caffrey, Peter Gmeiner, and Brian K. Kobilka, "Structure and Function of an Irreversible Agonist-β2 Adrenoceptor Complex," Nature, vol. 469, no. 7329, 2011, pp. 236–240. Text
Stefano Piana, Krishnarjun Sarkar, Kresten Lindorff-Larsen, Minghao Guo, Martin Gruebele, and David E. Shaw, "Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein," Journal of Molecular Biology, vol. 405, no. 1, 2011, pp. 43–48. Text
David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers, "Atomic-Level Characterization of the Structural Dynamics of Proteins," Science, vol. 330, no. 6002, 2010, pp. 341–346. Text
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, J.P. Grossman, Kenneth M. Mackenzie, Brian Towles, Edmond Chow, John K. Salmon, Cliff Young, Joseph A. Bank, Brannon Batson, Martin M. Deneroff, Jeffrey S. Kuskin, Richard H. Larson, Mark A. Moraes, and David E. Shaw, "Exploiting 162-Nanosecond End-to-End Communication Latency on Anton," Proceedings of the Conference for High Performance Computing, Networking, Storage and Analysis (SC10), New York, NY: IEEE, 2010. Text
Best Paper Award Finalist.
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), Berkeley, CA: USENIX Association, 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 Conference on High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY: ACM, 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 β2-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 Conference on High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY: ACM, 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), New York, NY: IEEE, 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), New York, NY: IEEE, 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), New York, NY: IEEE, 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), New York, NY: IEEE, 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), New York, NY: ACM, 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), New York, NY: ACM, 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), New York, NY: IEEE, 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