David E. Shaw - RankMe

50 papers A* 10A 13B 1C 4Misc 1Journal 19Unranked 1

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	Times Square Sampling: An Adaptive Algorithm for Free Energy Estimation. J. Comput. Graph. Stat. Cristian Predescu, Michael Snarski, Avi Robinson-Mosher, Duluxan Sritharan, Tamas Szalay, David E. Shaw
2023	J	`jnl`	A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. J. Chem. Inf. Model. Christine Y. Yeh, Jesus A. Izaguirre, Jack B. Greisman, Lindsay Willmore, Paul Maragakis, David E. Shaw
2023	J	`jnl`	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. Jack B. Greisman, Lindsay Willmore, Christine Y. Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter M. Nisonoff, Paul Maragakis, David E. Shaw
2022	J	`jnl`	How does a small molecule bind at a cryptic binding site? PLoS Comput. Biol. Yibing Shan, Venkatesh P. Mysore, Abba E. Leffler, Eric T. Kim, Shiori Sagawa, David E. Shaw
2022	A*	`conf`	The Specialized High-Performance Network on Anton 3. HPCA Keun Sup Shim, Brian Greskamp, Brian Towles, Bruce Edwards, J. P. Grossman, David E. Shaw
2022	J	`jnl`	The Specialized High-Performance Network on Anton 3. CoRR Keun Sup Shim, Brian Greskamp, Brian Towles, Bruce Edwards, J. P. Grossman, David E. Shaw
2021	A	`conf`	Anton 3: twenty microseconds of molecular dynamics simulation before lunch. SC 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
2021	—	`conf`	The ΛNTON 3 ASIC: a Fire-Breathing Monster for Molecular Dynamics Simulations. HCS 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
2020	J	`jnl`	A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery. J. Chem. Inf. Model. Paul Maragakis, Hunter M. Nisonoff, Brian Cole, David E. Shaw
2020	J	`jnl`	A deep-learning view of chemical space designed to facilitate drug discovery. CoRR Paul Maragakis, Hunter M. Nisonoff, Brian Cole, David E. Shaw
2020	J	`jnl`	AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. J. Chem. Inf. Model. Siduo Jiang, Miklos Feher, Christopher I. Williams, Brian Cole, David E. Shaw
2020	J	`jnl`	Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. CoRR John J. Cherian, Andrew G. Taube, Robert T. McGibbon, Panagiotis Angelikopoulos, Guy Blanc, Michael Snarski, Daniel D. Richman, John L. Klepeis, David E. Shaw
2018	J	`jnl`	Mechanism of NMDA receptor channel block by MK-801 and memantine. Nat. Xianqiang Song, Morten Ø. Jensen, Vishwanath Jogini, Richard A. Stein, Chia-Hsueh Lee, Hassane S. Mchaourab, David E. Shaw, Eric Gouaux
2015	A	`conf`	Filtering, Reductions and Synchronization in the Anton 2 Network. IPDPS J. P. Grossman, Brian Towles, Brian Greskamp, David E. Shaw
2014	A	`conf`	Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer. SC 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
2014	J	`jnl`	Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor. PLoS Comput. Biol. Anton Arkhipov, Yibing Shan, Eric T. Kim, David E. Shaw
2014	A*	`conf`	Unifying on-chip and inter-node switching within the Anton 2 network. ISCA Brian Towles, J. P. Grossman, Brian Greskamp, David E. Shaw
2013	B	`conf`	A detailed and flexible cycle-accurate Network-on-Chip simulator. ISPASS Nan Jiang, Daniel U. Becker, George Michelogiannakis, James D. Balfour, Brian Towles, David E. Shaw, John Kim, William J. Dally
2013	A	`conf`	Anton: a special-purpose machine that achieves a hundred-fold speedup in biomolecular simulations. HPDC David E. Shaw
2013	A	`conf`	Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine. IPDPS 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
2013	A*	`conf`	Hardware support for fine-grained event-driven computation in Anton 2. ASPLOS 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
2013	A*	`conf`	The role of cascade, a cycle-based simulation infrastructure, in designing the anton special-purpose supercomputers. DAC J. P. Grossman, Brian Towles, Joseph A. Bank, David E. Shaw
2012	J	`jnl`	The future of molecular dynamics simulations in drug discovery. J. Comput. Aided Mol. Des. David W. Borhani, David E. Shaw
2011	—	`ch.`	Anton, A Special-Purpose Molecular Simulation Machine. Encyclopedia of Parallel Computing Ron O. Dror, Cliff Young, David E. Shaw
2011	J	`jnl`	Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation. IEEE Micro 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
2011	A	`conf`	Parallel random numbers: as easy as 1, 2, 3. SC John K. Salmon, Mark A. Moraes, Ron O. Dror, David E. Shaw
2011	C	`conf`	Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots. IEEE Symposium on Computer Arithmetic J. Adam Butts, Ping Tak Peter Tang, Ron O. Dror, David E. Shaw
2011	C	`conf`	Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/sqrt(x) Design. IEEE Symposium on Computer Arithmetic Ping Tak Peter Tang, J. Adam Butts, Ron O. Dror, David E. Shaw
2010	A	`conf`	Accelerating Parallel Analysis of Scientific Simulation Data via Zazen. FAST Tiankai Tu, Charles A. Rendleman, Patrick J. Miller, Federico D. Sacerdoti, Ron O. Dror, David E. Shaw
2010	A	`conf`	Exploiting 162-Nanosecond End-to-End Communication Latency on Anton. SC 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
2010	J	`jnl`	Improved twiddle access for fast fourier transforms. IEEE Trans. Signal Process. Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, David E. Shaw
2009	A	`conf`	A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton. SC Cliff Young, Joseph A. Bank, Ron O. Dror, J. P. Grossman, John K. Salmon, David E. Shaw
2009	C	`conf`	Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins. IEEE Symposium on Computer Arithmetic David E. Shaw
2009	A	`conf`	Millisecond-scale molecular dynamics simulations on Anton. SC 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
2009	A	`conf`	Millisecond-scale molecular dynamics simulations on Anton. SC 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
2008	A	`conf`	A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. SC 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
2008	J	`jnl`	Anton, a special-purpose machine for molecular dynamics simulation. Commun. ACM 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
2008	A*	`conf`	Architectures and algorithms for millisecond-scale molecular dynamics simulations of proteins. MICRO David E. Shaw
2008	A*	`conf`	Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic. DAC C. Richard Ho, Michael Theobald, Martin M. Deneroff, Ron O. Dror, Joseph Gagliardo, David E. Shaw
2008	C	`conf`	Hierarchical simulation-based verification of Anton, a special-purpose parallel machine. ICCD 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
2008	A*	`conf`	High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. HPCA 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
2008	A*	`conf`	Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation. HPCA Jeffrey Kuskin, Cliff Young, J. P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, David E. Shaw
2008	Misc	`conf`	Simulation and embedded software development for Anton, a parallel machine with heterogeneous multicore ASICs. CODES+ISSS J. P. Grossman, Cliff Young, Joseph A. Bank, Kenneth M. Mackenzie, Doug Ierardi, John K. Salmon, Ron O. Dror, David E. Shaw
2007	A*	`conf`	Anton, a special-purpose machine for molecular dynamics simulation. ISCA 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
2007	J	`jnl`	Zonal methods for the parallel execution of range-limited N-body simulations. J. Comput. Phys. Kevin J. Bowers, Ron O. Dror, David E. Shaw
2006	A	`conf`	Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. SC 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
2006	J	`jnl`	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. Steven L. Dixon, Alexander M. Smondyrev, Eric H. Knoll, Shashidhar N. Rao, David E. Shaw, Richard A. Friesner
2005	J	`jnl`	A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. David E. Shaw
2005	J	`jnl`	Erraturm - A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J. Comput. Chem. David E. Shaw
1975	A*	`conf`	Inferring LISP Programs From Examples. IJCAI David E. Shaw, William R. Swartout, C. Cordell Green