David E. Shaw

Publication Activity (10 Years)

Years Active: 1975-2023
Publications (10 Years): 12

Top Topics

General Purpose

Protein Folding

Molecular Dynamics

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Jack B. Greisman, Lindsay Willmore, Christine Y. Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter M. Nisonoff, Paul Maragakis, David E. Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. J. Chem. Inf. Model. 63 (9) (2023)
Christine Y. Yeh, Jesus A. Izaguirre, Jack B. Greisman, Lindsay Willmore, Paul Maragakis, David E. Shaw
A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. J. Chem. Inf. Model. 63 (13) (2023)
Keun Sup Shim, Brian Greskamp, Brian Towles, Bruce Edwards, J. P. Grossman, David E. Shaw
The Specialized High-Performance Network on Anton 3. CoRR (2022)
Yibing Shan, Venkatesh P. Mysore, Abba E. Leffler, Eric T. Kim, Shiori Sagawa, David E. Shaw
How does a small molecule bind at a cryptic binding site? PLoS Comput. Biol. 18 (3) (2022)
Keun Sup Shim, Brian Greskamp, Brian Towles, Bruce Edwards, J. P. Grossman, David E. Shaw
The Specialized High-Performance Network on Anton 3. HPCA (2022)
David E. Shaw, Peter J. Adams, Asaph Azaria, Joseph A. Bank, Brannon Batson, Alistair Bell, Michael Bergdorf, Jhanvi Bhatt, J. Adam Butts, Timothy Correia, Robert M. Dirks, Ron O. Dror, Michael P. Eastwood, Bruce Edwards, Amos Even, Peter Feldmann, Michael Fenn, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Maria Gorlatova, Brian Greskamp, J. P. Grossman, Justin Gullingsrud, Anissa Harper, William Hasenplaugh, Mark Heily, Benjamin Colin Heshmat, Jeremy Hunt, Douglas J. Ierardi, Lev Iserovich, Bryan L. Jackson, Nick P. Johnson, Mollie M. Kirk, John L. Klepeis, Jeffrey S. Kuskin, Kenneth M. Mackenzie, Roy J. Mader, Richard McGowen, Adam McLaughlin, Mark A. Moraes, Mohamed H. Nasr, Lawrence J. Nociolo, Lief O'Donnell, Andrew Parker, Jon L. Peticolas, Goran Pocina, Cristian Predescu, Terry Quan, John K. Salmon, Carl Schwink, Keun Sup Shim, Naseer Siddique, Jochen Spengler, Tamas Szalay, Raymond Tabladillo, Reinhard Tartler, Andrew G. Taube, Michael Theobald, Brian Towles, William Vick, Stanley C. Wang, Michael Wazlowski, Madeleine J. Weingarten, John M. Williams, Kevin A. Yuh
Anton 3: twenty microseconds of molecular dynamics simulation before lunch. SC (2021)
Peter J. Adams, Brannon Batson, Alistair Bell, Jhanvi Bhatt, J. Adam Butts, Timothy Correia, Bruce Edwards, Peter Feldmann, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Maria Gorlatova, Brian Greskamp, J. P. Grossman, Jeremy Hunt, Bryan L. Jackson, Mollie M. Kirk, Jeffrey Kuskin, Roy J. Mader, Richard McGowen, Adam McLaughlin, Mark A. Moraes, Mohamed Nasr, Lawrence J. Nociolo, Lief O'Donnell, Andrew Parker, Jon L. Peticolas, Terry Quan, T. Carl Schwink, Keun Sup Shim, Naseer Siddique, Jochen Spengler, Michael Theobald, Brian Towles, William Vick, Stanley C. Wang, Michael E. Wazlowski, Madeleine J. Weingarten, John M. Williams, David E. Shaw
The ΛNTON 3 ASIC: a Fire-Breathing Monster for Molecular Dynamics Simulations. HCS (2021)
John J. Cherian, Andrew G. Taube, Robert T. McGibbon, Panagiotis Angelikopoulos, Guy Blanc, Michael Snarski, Daniel D. Richman, John L. Klepeis, David E. Shaw
Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. CoRR (2020)
Paul Maragakis, Hunter M. Nisonoff, Brian Cole, David E. Shaw
A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery. J. Chem. Inf. Model. 60 (10) (2020)
Siduo Jiang, Miklos Feher, Christopher I. Williams, Brian Cole, David E. Shaw
AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. J. Chem. Inf. Model. 60 (9) (2020)
Paul Maragakis, Hunter M. Nisonoff, Brian Cole, David E. Shaw
A deep-learning view of chemical space designed to facilitate drug discovery. CoRR (2020)
Xianqiang Song, Morten Ø. Jensen, Vishwanath Jogini, Richard A. Stein, Chia-Hsueh Lee, Hassane S. Mchaourab, David E. Shaw, Eric Gouaux
Mechanism of NMDA receptor channel block by MK-801 and memantine. Nat. 556 (7702) (2018)
J. P. Grossman, Brian Towles, Brian Greskamp, David E. Shaw
Filtering, Reductions and Synchronization in the Anton 2 Network. IPDPS (2015)
David E. Shaw, J. P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, Ron O. Dror, Amos Even, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Brian Greskamp, Richard C. Ho, Douglas J. Ierardi, Lev Iserovich, Jeffrey Kuskin, Richard H. Larson, Timothy Layman, Li-Siang Lee, Adam K. Lerer, Chester Li, Daniel Killebrew, Kenneth M. Mackenzie, Shark Yeuk-Hai Mok, Mark A. Moraes, Rolf Mueller, Lawrence J. Nociolo, Jon L. Peticolas, Terry Quan, Daniel Ramot, John K. Salmon, Daniele Paolo Scarpazza, U. Ben Schafer, Naseer Siddique, Christopher W. Snyder, Jochen Spengler, Ping Tak Peter Tang, Michael Theobald, Horia Toma, Brian Towles, Benjamin Vitale, Stanley C. Wang, Cliff Young
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer. SC (2014)
Brian Towles, J. P. Grossman, Brian Greskamp, David E. Shaw
Unifying on-chip and inter-node switching within the Anton 2 network. ISCA (2014)
Anton Arkhipov, Yibing Shan, Eric T. Kim, David E. Shaw
Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor. PLoS Comput. Biol. 10 (7) (2014)
J. P. Grossman, Jeffrey Kuskin, Joseph A. Bank, Michael Theobald, Ron O. Dror, Douglas J. Ierardi, Richard H. Larson, U. Ben Schafer, Brian Towles, Cliff Young, David E. Shaw
Hardware support for fine-grained event-driven computation in Anton 2. ASPLOS (2013)
David E. Shaw
Anton: a special-purpose machine that achieves a hundred-fold speedup in biomolecular simulations. HPDC (2013)
Daniele Paolo Scarpazza, Douglas J. Ierardi, Adam K. Lerer, Kenneth M. Mackenzie, Albert C. Pan, Joseph A. Bank, Edmond Chow, Ron O. Dror, J. P. Grossman, Daniel Killebrew, Mark A. Moraes, Cristian Predescu, John K. Salmon, David E. Shaw
Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine. IPDPS (2013)
Nan Jiang, Daniel U. Becker, George Michelogiannakis, James D. Balfour, Brian Towles, David E. Shaw, John Kim, William J. Dally
A detailed and flexible cycle-accurate Network-on-Chip simulator. ISPASS (2013)
J. P. Grossman, Brian Towles, Joseph A. Bank, David E. Shaw
The role of cascade, a cycle-based simulation infrastructure, in designing the anton special-purpose supercomputers. DAC (2013)
David W. Borhani, David E. Shaw
The future of molecular dynamics simulations in drug discovery. J. Comput. Aided Mol. Des. 26 (1) (2012)
J. Adam Butts, Ping Tak Peter Tang, Ron O. Dror, David E. Shaw
Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots. IEEE Symposium on Computer Arithmetic (2011)
Ping Tak Peter Tang, J. Adam Butts, Ron O. Dror, David E. Shaw
Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/sqrt(x) Design. IEEE Symposium on Computer Arithmetic (2011)
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 Kuskin, Richard H. Larson, Mark A. Moraes, David E. Shaw
Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation. IEEE Micro 31 (3) (2011)
John K. Salmon, Mark A. Moraes, Ron O. Dror, David E. Shaw
Parallel random numbers: as easy as 1, 2, 3. SC (2011)
Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, David E. Shaw
Improved twiddle access for fast fourier transforms. IEEE Trans. Signal Process. 58 (3) (2010)
Tiankai Tu, Charles A. Rendleman, Patrick J. Miller, Federico D. Sacerdoti, Ron O. Dror, David E. Shaw
Accelerating Parallel Analysis of Scientific Simulation Data via Zazen. FAST (2010)
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 Kuskin, Richard H. Larson, Mark A. Moraes, David E. Shaw
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton. SC (2010)
Cliff Young, Joseph A. Bank, Ron O. Dror, J. P. Grossman, John K. Salmon, David E. Shaw
A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton. SC (2009)
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, Doug Ierardi, John L. Klepeis, Jeffrey Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, Brian Towles
Millisecond-scale molecular dynamics simulations on Anton. SC (2009)
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, Doug Ierardi, John L. Klepeis, Jeffrey Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, Brian Towles
Millisecond-scale molecular dynamics simulations on Anton. SC (2009)
David E. Shaw
Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins. IEEE Symposium on Computer Arithmetic (2009)
Jeffrey Kuskin, Cliff Young, J. P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, David E. Shaw
Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation. HPCA (2008)
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey 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, Richard C. Ho, Doug 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, Stanley C. Wang
Anton, a special-purpose machine for molecular dynamics simulation. Commun. ACM 51 (7) (2008)
J. P. Grossman, Cliff Young, Joseph A. Bank, Kenneth M. Mackenzie, Doug Ierardi, John K. Salmon, Ron O. Dror, David E. Shaw
Simulation and embedded software development for Anton, a parallel machine with heterogeneous multicore ASICs. CODES+ISSS (2008)
Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J. P. Grossman, Yibing Shan, John L. Klepeis, David E. Shaw
High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. HPCA (2008)
J. P. Grossman, John K. Salmon, Richard C. Ho, Doug Ierardi, Brian Towles, Brannon Batson, Jochen Spengler, Stanley C. Wang, Rolf Mueller, Michael Theobald, Cliff Young, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, David E. Shaw
Hierarchical simulation-based verification of Anton, a special-purpose parallel machine. ICCD (2008)
Richard C. Ho, Michael Theobald, Martin M. Deneroff, Ron O. Dror, Joseph Gagliardo, David E. Shaw
Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic. DAC (2008)
Tiankai Tu, Charles A. Rendleman, David W. Borhani, Ron O. Dror, Justin Gullingsrud, Morten Ø. Jensen, John L. Klepeis, Paul Maragakis, Patrick J. Miller, Kate A. Stafford, David E. Shaw
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. SC (2008)
David E. Shaw
Architectures and algorithms for millisecond-scale molecular dynamics simulations of proteins. MICRO (2008)
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey 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, Richard C. Ho, Doug 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, Stanley C. Wang
Anton, a special-purpose machine for molecular dynamics simulation. ISCA (2007)
Kevin J. Bowers, Ron O. Dror, David E. Shaw
Zonal methods for the parallel execution of range-limited N-body simulations. J. Comput. Phys. 221 (1) (2007)
Steven L. Dixon, Alexander M. Smondyrev, Eric H. Knoll, Shashidhar N. Rao, David E. Shaw, Richard A. Friesner
PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J. Comput. Aided Mol. Des. 20 (10-11) (2006)
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
Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. SC (2006)
David E. Shaw
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. 26 (13) (2005)
David E. Shaw
Erraturm - A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. 26 (16) (2005)
David E. Shaw, William R. Swartout, C. Cordell Green
Inferring LISP Programs From Examples. IJCAI (1975)