Inferring LISP Programs From Examples. - David E. Shaw; William R. Swartout; C. Cordell Green (IJCAI, 1975)

A Relational Database Machine Architecture. - David Elliot Shaw (SIGMOD Rec., 1980)

NON-VON: A Parallel Machine Architecture for Knowledge-Based Information Processing. - David Elliot Shaw (IJCAI, 1981)

The NON-VON Database Machine: A Brief Overview. - David Elliot Shaw; Salvatore J. Stolfo; Hussein Ibrahim; Bruce Hillyer; Gio Wiederhold; J. A. Andrews (IEEE Database Eng. Bull., 1981)

DADO: A Tree-Structured Machine Architecture for Production Systems. - Salvatore J. Stolfo; David Elliot Shaw (AAAI, 1982)

Architecture and Applications of DADO: A Large-Scale Parallel Computer for Artificial Intelligence. - Salvatore J. Stolfo; Daniel P. Miranker; David Elliot Shaw (IJCAI, 1983)

SIMD and MSIMD Variants of the NON-VON Supercomputer. - David Elliot Shaw (COMPCON, 1984)

The semi-automatic generation of processing element control paths for highly parallel machines. - Theodore Sabety; David Elliot Shaw; Brian Mathies (DAC, 1984)

Relational Query Processing on the Non-Von Supercomputer. - David Elliot Shaw (Query Processing in Database Systems, 1985)

NON-VONs Applicability to Three AI Task Areas. - David Elliot Shaw (IJCAI, 1985)

The multiple-processor PPS chip of the NON-VON 3 supercomputer. - David Elliot Shaw; Theodore Sabety (Integr., 1985)

SIMD Tree Algorithms for Image Correlation. - Hussein Ibrahim; John R. Kender; David Elliot Shaw (AAAI, 1986)

On the application of massively parallel SIMD tree machines to certain intermediate-level vision tasks. - Hussein A. H. Ibrahim; John R. Kender; David Elliot Shaw (Comput. Vis. Graph. Image Process., 1986)

Execution of OPS5 Production Systems on a Massively Parallel Machine. - Bruce Hillyer; David Elliot Shaw (J. Parallel Distributed Comput., 1986)

NON-VON's Performance on Certain Database Benchmarks. - Bruce Hillyer; David Elliot Shaw; Anil Nigam (IEEE Trans. Software Eng., 1986)

On the Range of Applicability of an Artificial Intelligence Machine. - David Elliot Shaw (Artif. Intell., 1987)

Low-Level Image Analysis Tasks on Fine-Grained Tree-Structured SIMD Machines. - Hussein Ibrahim; John R. Kender; David Elliot Shaw (J. Parallel Distributed Comput., 1987)

Technology and the Future of Commerce and Finance (Abstract). - David Elliot Shaw (VLDB, 1998)

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. - David E. Shaw (J. Comput. Chem., 2005)

Erraturm - A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. - David E. Shaw (J. Comput. Chem., 2005)

Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters. - 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; et al. (SC, 2006)

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. - Steven L. Dixon; Alexander M. Smondyrev; Eric H. Knoll; Shashidhar N. Rao; David E. Shaw; Richard A. Friesner (J. Comput. Aided Mol. Des., 2006)

Zonal methods for the parallel execution of range-limited N-body simulations. - Kevin J. Bowers; Ron O. Dror; David E. Shaw (J. Comput. Phys., 2007)

Simulation and embedded software development for Anton, a parallel machine with heterogeneous multicore ASICs. - J. P. Grossman; Cliff Young; Joseph A. Bank; Kenneth M. Mackenzie; Doug Ierardi; John K. Salmon; Ron O. Dror; David E. Shaw (CODES+ISSS, 2008)

Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic. - C. Richard Ho; Michael Theobald; Martin M. Deneroff; Ron O. Dror; Joseph Gagliardo; David E. Shaw (DAC, 2008)

Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation. - Jeffrey Kuskin; Cliff Young; J. P. Grossman; Brannon Batson; Martin M. Deneroff; Ron O. Dror; David E. Shaw (HPCA, 2008)

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. - 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 (HPCA, 2008)

Hierarchical simulation-based verification of Anton, a special-purpose parallel machine. - 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; et al. (ICCD, 2008)

Architectures and algorithms for millisecond-scale molecular dynamics simulations of proteins. - David E. Shaw (MICRO, 2008)

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. - 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 (SC, 2008)

Anton, a special-purpose machine for molecular dynamics simulation. - 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; et al. (Commun. ACM, 2008)

Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins. - David E. Shaw (IEEE Symposium on Computer Arithmetic, 2009)

Millisecond-scale molecular dynamics simulations on Anton. - 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; et al. (SC, 2009)

A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton. - Cliff Young; Joseph A. Bank; Ron O. Dror; J. P. Grossman; John K. Salmon; David E. Shaw (SC, 2009)

Accelerating Parallel Analysis of Scientific Simulation Data via Zazen. - Tiankai Tu; Charles A. Rendleman; Patrick J. Miller; Federico D. Sacerdoti; Ron O. Dror; David E. Shaw (FAST, 2010)

Exploiting 162-Nanosecond End-to-End Communication Latency on Anton. - 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; et al. (SC, 2010)

Improved twiddle access for fast fourier transforms. - Kevin J. Bowers; Ross A. Lippert; Ron O. Dror; David E. Shaw (IEEE Trans. Signal Process., 2010)

Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots. - J. Adam Butts; Ping Tak Peter Tang; Ron O. Dror; David E. Shaw (IEEE Symposium on Computer Arithmetic, 2011)

Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/sqrt(x) Design. - Ping Tak Peter Tang; J. Adam Butts; Ron O. Dror; David E. Shaw (IEEE Symposium on Computer Arithmetic, 2011)

Parallel random numbers: as easy as 1, 2, 3. - John K. Salmon; Mark A. Moraes; Ron O. Dror; David E. Shaw (SC, 2011)

Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation. - 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; et al. (IEEE Micro, 2011)

Anton, A Special-Purpose Molecular Simulation Machine. - Ron O. Dror; Cliff Young; David E. Shaw (Encyclopedia of Parallel Computing, 2011)

The future of molecular dynamics simulations in drug discovery. - David W. Borhani; David E. Shaw (J. Comput. Aided Mol. Des., 2012)

Hardware support for fine-grained event-driven computation in Anton 2. - 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 (ASPLOS, 2013)

The role of cascade, a cycle-based simulation infrastructure, in designing the anton special-purpose supercomputers. - J. P. Grossman; Brian Towles; Joseph A. Bank; David E. Shaw (DAC, 2013)

Anton: a special-purpose machine that achieves a hundred-fold speedup in biomolecular simulations. - David E. Shaw (HPDC, 2013)

Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine. - 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; et al. (IPDPS, 2013)

A detailed and flexible cycle-accurate Network-on-Chip simulator. - Nan Jiang 009; Daniel U. Becker; George Michelogiannakis; James D. Balfour; Brian Towles; David E. Shaw; John Kim 001; William J. Dally (ISPASS, 2013)

Unifying on-chip and inter-node switching within the Anton 2 network. - Brian Towles; J. P. Grossman; Brian Greskamp; David E. Shaw (ISCA, 2014)

Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer. - 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; et al. (SC, 2014)

Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor. - Anton Arkhipov; Yibing Shan; Eric T. Kim; David E. Shaw (PLoS Comput. Biol., 2014)

Filtering, Reductions and Synchronization in the Anton 2 Network. - J. P. Grossman; Brian Towles; Brian Greskamp; David E. Shaw (IPDPS, 2015)

Mechanism of NMDA receptor channel block by MK-801 and memantine. - Xianqiang Song; Morten Ø. Jensen; Vishwanath Jogini; Richard A. Stein; Chia-Hsueh Lee; Hassane S. Mchaourab; David E. Shaw; Eric Gouaux (Nat., 2018)

Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. - John J. Cherian; Andrew G. Taube; Robert T. McGibbon; Panagiotis Angelikopoulos; Guy Blanc; Michael Snarski; Daniel D. Richman; John L. Klepeis; David E. Shaw (CoRR, 2020)

AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. - Siduo Jiang; Miklos Feher; Christopher I. Williams; Brian Cole; David E. Shaw (J. Chem. Inf. Model., 2020)

A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery. - Paul Maragakis; Hunter M. Nisonoff; Brian Cole; David E. Shaw (J. Chem. Inf. Model., 2020)

The ΛNTON 3 ASIC: a Fire-Breathing Monster for Molecular Dynamics Simulations. - 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; et al. (HCS, 2021)

Anton 3: twenty microseconds of molecular dynamics simulation before lunch. - 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; et al. (SC, 2021)

The Specialized High-Performance Network on Anton 3. - Keun Sup Shim; Brian Greskamp; Brian Towles; Bruce Edwards; J. P. Grossman; David E. Shaw (HPCA, 2022)

How does a small molecule bind at a cryptic binding site? - Yibing Shan; Venkatesh P. Mysore; Abba E. Leffler; Eric T. Kim; Shiori Sagawa; David E. Shaw (PLoS Comput. Biol., 2022)

Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. - Jack B. Greisman; Lindsay Willmore; Christine Y. Yeh; Fabrizio Giordanetto; Sahar Shahamadtar; Hunter M. Nisonoff; Paul Maragakis; David E. Shaw (J. Chem. Inf. Model., 2023)

A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. - Christine Y. Yeh; Jesus A. Izaguirre; Jack B. Greisman; Lindsay Willmore; Paul Maragakis; David E. Shaw (J. Chem. Inf. Model., 2023)

Times Square Sampling: An Adaptive Algorithm for Free Energy Estimation. - Cristian Predescu; Michael Snarski; Avi Robinson-Mosher; Duluxan Sritharan; Tamas Szalay; David E. Shaw (J. Comput. Graph. Stat., 2024)