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2020 – today
- 2023
[c28]Minkai Xu, Alexander S. Powers, Ron O. Dror, Stefano Ermon, Jure Leskovec:
Geometric Latent Diffusion Models for 3D Molecule Generation. ICML 2023: 38592-38610- [i11]Christopher Fifty, Joseph M. Paggi, Ehsan Amid, Jure Leskovec, Ron O. Dror:
Harnessing Simulation for Molecular Embeddings. CoRR abs/2302.02055 (2023) - [i10]Patricia Suriana, Joseph M. Paggi, Ron O. Dror:
FlexVDW: A machine learning approach to account for protein flexibility in ligand docking. CoRR abs/2303.11494 (2023) - [i9]Minkai Xu, Alexander S. Powers, Ron O. Dror, Stefano Ermon, Jure Leskovec:
Geometric Latent Diffusion Models for 3D Molecule Generation. CoRR abs/2305.01140 (2023) - [i8]Patricia Suriana, Ron O. Dror:
Enhancing Ligand Pose Sampling for Molecular Docking. CoRR abs/2312.00191 (2023) - 2021
- [j7]Brendan Kelly, Scott A. Hollingsworth
, David C. Blakemore, Robert M. Owen, R. Ian Storer, Nigel A. Swain, Deniz Aydin, Rubben Torella, Joseph S. Warmus, Ron O. Dror:
Delineating the Ligand-Receptor Interactions That Lead to Biased Signaling at the μ-Opioid Receptor. J. Chem. Inf. Model. 61(7): 3696-3707 (2021) - [c27]Bowen Jing, Stephan Eismann, Patricia Suriana, Raphael John Lamarre Townshend, Ron O. Dror:
Learning from Protein Structure with Geometric Vector Perceptrons. ICLR 2021 - [c26]Raphael J. L. Townshend, Martin Vögele, Patricia Suriana, Alexander Derry, Alexander S. Powers, Yianni Laloudakis, Sidhika Balachandar, Bowen Jing, Brandon M. Anderson, Stephan Eismann, Risi Kondor, Russ B. Altman, Ron O. Dror:
ATOM3D: Tasks on Molecules in Three Dimensions. NeurIPS Datasets and Benchmarks 2021 - [c25]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 - [i7]Bowen Jing, Stephan Eismann, Pratham N. Soni, Ron O. Dror:
Equivariant Graph Neural Networks for 3D Macromolecular Structure. CoRR abs/2106.03843 (2021) - 2020
- [i6]Stephan Eismann, Raphael J. L. Townshend, Nathaniel Thomas, Milind Jagota, Bowen Jing, Ron O. Dror:
Hierarchical, rotation-equivariant neural networks to predict the structure of protein complexes. CoRR abs/2006.09275 (2020) - [i5]Raphael J. L. Townshend, Brent Townshend, Stephan Eismann, Ron O. Dror:
Geometric Prediction: Moving Beyond Scalars. CoRR abs/2006.14163 (2020) - [i4]Bowen Jing, Stephan Eismann, Patricia Suriana, Raphael J. L. Townshend, Ron O. Dror:
Learning from Protein Structure with Geometric Vector Perceptrons. CoRR abs/2009.01411 (2020) - [i3]Stephan Eismann, Patricia Suriana, Bowen Jing, Raphael J. L. Townshend, Ron O. Dror:
Protein model quality assessment using rotation-equivariant, hierarchical neural networks. CoRR abs/2011.13557 (2020) - [i2]Raphael J. L. Townshend, Martin Vögele, Patricia Suriana, Alexander Derry, Alexander S. Powers, Yianni Laloudakis, Sidhika Balachandar, Brandon M. Anderson, Stephan Eismann, Risi Kondor, Russ B. Altman, Ron O. Dror:
ATOM3D: Tasks On Molecules in Three Dimensions. CoRR abs/2012.04035 (2020)
2010 – 2019
- 2019
- [c24]Raphael J. L. Townshend, Rishi Bedi, Patricia Suriana, Ron O. Dror:
End-to-End Learning on 3D Protein Structure for Interface Prediction. NeurIPS 2019: 15616-15625 - 2018
- [i1]Raphael J. L. Townshend, Rishi Bedi, Ron O. Dror:
Generalizable Protein Interface Prediction with End-to-End Learning. CoRR abs/1807.01297 (2018) - 2016
- [j6]Samuel Hertig, Naomi R. Latorraca, Ron O. Dror:
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations. PLoS Comput. Biol. 12(6) (2016) - 2014
- [c23]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
- [c22]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 - [c21]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 - 2011
- [j5]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) - [c20]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 - [c19]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 - [c18]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
- [j4]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) - [c17]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 - [c16]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
- [c15]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 - [c14]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 - [c13]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
- [j3]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) - [c12]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 - [c11]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 - [c10]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 - [c9]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 - [c8]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 - [c7]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
- [j2]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) - [c6]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
- [c5]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 - 2003
- [j1]Ron O. Dror, Jonathan G. Murnick, Nicola J. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, Richard A. Young:
Bayesian Estimation of Transcript Levels Using a General Model of Array Measurement Noise. J. Comput. Biol. 10(3/4): 433-452 (2003) - 2002
- [b1]Ron O. Dror:
Surface reflectance recognition and real-world illumination statistics. Massachusetts Institute of Technology, Cambridge, MA, USA, 2002 - [c4]Ron O. Dror, Jonathan G. Murnick, Nicola A. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, Richard A. Young:
A bayesian approach to transcript estimation from gene array data: the BEAM technique. RECOMB 2002: 137-143 - 2001
- [c3]Ron O. Dror, Thomas K. Leung, Edward H. Adelson, Alan S. Willsky:
Statistics of Real-World Illumination. CVPR (2) 2001: 164-171 - [c2]Ron O. Dror, Edward H. Adelson, Alan S. Willsky:
Estimating surface reflectance properties from images under unknown illumination. Human Vision and Electronic Imaging 2001: 231-242 - 2000
- [c1]Ron O. Dror, David C. O'Carroll, Simon B. Laughlin:
The Role of Natural Image Statistics in Biological Motion Estimation. Biologically Motivated Computer Vision 2000: 492-501
Coauthor Index
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