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ORCIDDavid E. Shaw
David Elliot Shaw
Person information
- affiliation: Columbia University, New York, NY, USA
- affiliation: D. E. Shaw Research
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2020 – today
- 2023
[j22]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): 2644-2650 (2023)- [j21]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): 4115-4124 (2023) - 2022
- [j20]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) - [c39]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: 1211-1223 - [i3]Keun Sup Shim, Brian Greskamp, Brian Towles, Bruce Edwards, J. P. Grossman, David E. Shaw:
The Specialized High-Performance Network on Anton 3. CoRR abs/2201.08357 (2022) - 2021
- [c38]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: 1-22 - [c37]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: 1 - 2020
- [j19]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): 4326-4338 (2020) - [j18]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): 4487-4496 (2020) - [i2]Paul Maragakis, Hunter M. Nisonoff, Brian Cole, David E. Shaw:
A deep-learning view of chemical space designed to facilitate drug discovery. CoRR abs/2002.02948 (2020) - [i1]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 abs/2008.06431 (2020)
2010 – 2019
- 2018
- [j17]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): 515-519 (2018) - 2015
- [c36]J. P. Grossman, Brian Towles, Brian Greskamp, David E. Shaw:
Filtering, Reductions and Synchronization in the Anton 2 Network. IPDPS 2015: 860-870 - 2014
- [j16]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) - [c35]Brian Towles, J. P. Grossman, Brian Greskamp, David E. Shaw:
Unifying on-chip and inter-node switching within the Anton 2 network. ISCA 2014: 1-12 - [c34]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, C. Richard 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: 41-53 - 2013
- [c33]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: 549-560 - [c32]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: 122:1-122:9 - [c31]David E. Shaw:
Anton: a special-purpose machine that achieves a hundred-fold speedup in biomolecular simulations. HPDC 2013: 129-130 - [c30]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: 933-945 - [c29]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: 86-96 - 2012
- [j15]David W. Borhani, David E. Shaw:
The future of molecular dynamics simulations in drug discovery. J. Comput. Aided Mol. Des. 26(1): 15-26 (2012) - 2011
- [j14]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): 8-19 (2011) - [c28]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: 149-158 - [c27]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: 159-168 - [c26]John K. Salmon, Mark A. Moraes, Ron O. Dror, David E. Shaw:
Parallel random numbers: as easy as 1, 2, 3. SC 2011: 16:1-16:12 - [r1]Ron O. Dror, Cliff Young, David E. Shaw:
Anton, A Special-Purpose Molecular Simulation Machine. Encyclopedia of Parallel Computing 2011: 60-71 - 2010
- [j13]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): 1122-1130 (2010) - [c25]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: 129-142 - [c24]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: 1-12
2000 – 2009
- 2009
- [c23]David E. Shaw:
Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins. IEEE Symposium on Computer Arithmetic 2009: 3 - [c22]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 - [c21]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 - [c20]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 - 2008
- [j12]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, C. Richard 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): 91-97 (2008) - [c19]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: 125-130 - [c18]C. Richard 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: 268-271 - [c17]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: 331-342 - [c16]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: 343-354 - [c15]J. P. Grossman, John K. Salmon, C. Richard 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: 340-347 - [c14]David E. Shaw:
Architectures and algorithms for millisecond-scale molecular dynamics simulations of proteins. MICRO 2008 - [c13]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: 56 - 2007
- [j11]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): 303-329 (2007) - [c12]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, C. Richard 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: 1-12 - 2006
- [j10]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): 647-671 (2006) - [c11]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: 84 - 2005
- [j9]David E. Shaw:
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. 26(13): 1318-1328 (2005) - [j8]David E. Shaw:
Erraturm - A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. 26(16): 1803 (2005)
1990 – 1999
- 1998
- [c10]David Elliot Shaw:
Technology and the Future of Commerce and Finance (Abstract). VLDB 1998: 13
1980 – 1989
- 1987
- [j7]David Elliot Shaw:
On the Range of Applicability of an Artificial Intelligence Machine. Artif. Intell. 32(2): 151-172 (1987) - [j6]Hussein Ibrahim, John R. Kender, David Elliot Shaw:
Low-Level Image Analysis Tasks on Fine-Grained Tree-Structured SIMD Machines. J. Parallel Distributed Comput. 4(6): 546-574 (1987) - 1986
- [j5]Hussein A. H. Ibrahim, John R. Kender, David Elliot Shaw:
On the application of massively parallel SIMD tree machines to certain intermediate-level vision tasks. Comput. Vis. Graph. Image Process. 36(1): 53-75 (1986) - [j4]Bruce Hillyer, David Elliot Shaw:
Execution of OPS5 Production Systems on a Massively Parallel Machine. J. Parallel Distributed Comput. 3(2): 236-268 (1986) - [j3]Bruce Hillyer, David Elliot Shaw, Anil Nigam:
NON-VON's Performance on Certain Database Benchmarks. IEEE Trans. Software Eng. 12(4): 577-583 (1986) - [c9]Hussein Ibrahim, John R. Kender, David Elliot Shaw:
SIMD Tree Algorithms for Image Correlation. AAAI 1986: 645-651 - 1985
- [j2]David Elliot Shaw, Theodore Sabety:
The multiple-processor PPS chip of the NON-VON 3 supercomputer. Integr. 3(3): 161-174 (1985) - [c8]David Elliot Shaw:
NON-VONs Applicability to Three AI Task Areas. IJCAI 1985: 61-72 - [p1]David Elliot Shaw:
Relational Query Processing on the Non-Von Supercomputer. Query Processing in Database Systems 1985: 248-258 - 1984
- [c7]David Elliot Shaw:
SIMD and MSIMD Variants of the NON-VON Supercomputer. COMPCON 1984: 360-363 - [c6]Theodore Sabety, David Elliot Shaw, Brian Mathies:
The semi-automatic generation of processing element control paths for highly parallel machines. DAC 1984: 441-446 - 1983
- [c5]Salvatore J. Stolfo, Daniel P. Miranker, David Elliot Shaw:
Architecture and Applications of DADO: A Large-Scale Parallel Computer for Artificial Intelligence. IJCAI 1983: 850-854 - 1982
- [c4]Salvatore J. Stolfo, David Elliot Shaw:
DADO: A Tree-Structured Machine Architecture for Production Systems. AAAI 1982: 242-246 - 1981
- [j1]David Elliot Shaw, Salvatore J. Stolfo, Hussein Ibrahim, Bruce Hillyer, Gio Wiederhold, J. A. Andrews:
The NON-VON Database Machine: A Brief Overview. IEEE Database Eng. Bull. 4(2): 41-52 (1981) - [c3]David Elliot Shaw:
NON-VON: A Parallel Machine Architecture for Knowledge-Based Information Processing. IJCAI 1981: 961-963 - 1980
- [c2]David Elliot Shaw:
A Relational Database Machine Architecture. Computer Architecture for Non-Numeric Processing 1980: 84-95
1970 – 1979
- 1975
- [c1]David E. Shaw, William R. Swartout, C. Cordell Green:
Inferring LISP Programs From Examples. IJCAI 1975: 260-267
Coauthor Index
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