Ron O. Dror

发表

Bayesian Estimation of Transcript Levels Using a General Model of Array Measurement Noise

Ron O. Dror, Jonathan G. Murnick, Nicola J. Rinaldi, 2003, J. Comput. Biol..

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

Ron O. Dror, Samuel Hertig, Naomi R. Latorraca, 2016, PLoS Comput. Biol..

Exploiting 162-Nanosecond End-to-End Communication Latency on Anton

Edmond Chow, J. P. Grossman, Brian Towles, 2010, 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis.

Accelerating Parallel Analysis of Scientific Simulation Data via Zazen

David E. Shaw, Ron O. Dror, Federico D. Sacerdoti, 2010, FAST.

Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic

David E. Shaw, Ron O. Dror, Michael Theobald, 2008, 2008 45th ACM/IEEE Design Automation Conference.

Anton, a special-purpose machine for molecular dynamics simulation

John L. Klepeis, J. P. Grossman, Brian Towles, 2007, ISCA '07.

Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation

J. P. Grossman, David E. Shaw, Ron O. Dror, 2008, 2008 IEEE 14th International Symposium on High Performance Computer Architecture.

Anton, A Special-Purpose Molecular Simulation Machine

David E. Shaw, Ron O. Dror, Cliff Young, 2011, Encyclopedia of Parallel Computing.

Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/sqrt(x) Design

David E. Shaw, Ping Tak Peter Tang, Ron O. Dror, 2011, 2011 IEEE 20th Symposium on Computer Arithmetic.

Zonal methods for the parallel execution of range-limited N-body simulations

David E. Shaw, Ron O. Dror, Kevin J. Bowers, 2007, J. Comput. Phys..

Surface reflectance recognition and real-world illumination statistics

Ron O. Dror, R. Dror, 2002 .

Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine

Edmond Chow, J. P. Grossman, Joseph A. Bank, 2013, 2013 IEEE 27th International Symposium on Parallel and Distributed Processing.

Simulation and embedded software development for Anton, a parallel machine with heterogeneous multicore ASICs

J. P. Grossman, Joseph A. Bank, David E. Shaw, 2008, CODES+ISSS '08.

Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation

Edmond Chow, J. P. Grossman, Brian Towles, 2011, IEEE Micro.

Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots

David E. Shaw, Ping Tak Peter Tang, Ron O. Dror, 2011, 2011 IEEE 20th Symposium on Computer Arithmetic.

Estimating surface reflectance properties from images under unknown illumination

Edward H. Adelson, Alan S. Willsky, Ron O. Dror, 2001, IS&T/SPIE Electronic Imaging.

Hardware support for fine-grained event-driven computation in Anton 2

J. P. Grossman, Brian Towles, Joseph A. Bank, 2013, ASPLOS '13.

Statistics of real-world illumination

Edward H. Adelson, Alan S. Willsky, Thomas K. Leung, 2001, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001.

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

John L. Klepeis, David E. Shaw, Ron O. Dror, 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

Hierarchical simulation-based verification of Anton, a special-purpose parallel machine

J. P. Grossman, Brian Towles, David E. Shaw, 2008, 2008 IEEE International Conference on Computer Design.

Improved Twiddle Access for Fast Fourier Transforms

David E. Shaw, Ron O. Dror, Kevin J. Bowers, 2010, IEEE Transactions on Signal Processing.

Millisecond-scale molecular dynamics simulations on Anton

John L. Klepeis, Kresten Lindorff-Larsen, Edmond Chow, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Anton: A specialized ASIC for molecular dynamics

David E. Shaw, Ron O. Dror, John K. Salmon, 2008, 2008 IEEE Hot Chips 20 Symposium (HCS).

Molecular dynamics - Scalable algorithms for molecular dynamics simulations on commodity clusters

John L. Klepeis, Edmond Chow, David E. Shaw, 2006, SC.

Elucidating membrane protein function through long-timescale molecular dynamics simulation

David E. Shaw, Ron O. Dror, Morten O. Jensen, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Automated Event Detection and Activity Monitoring in Long Time-Scale Molecular Dynamics

David E. Shaw, Ron O. Dror, Willy Wriggers, 2009 .

High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation

John L. Klepeis, J. P. Grossman, David E. Shaw, 2008, 2008 IEEE 14th International Symposium on High Performance Computer Architecture.

Generalizable Protein Interface Prediction with End-to-End Learning pdf

Ron O. Dror, Rishi Bedi, Raphael J. L. Townshend, 2018, ArXiv.

Correction: Systematic Validation of Protein Force Fields against Experimental Data

David E. Shaw, Ron O. Dror, Stefano Piana, 2013, PLoS ONE.

Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer

J. P. Grossman, Brian Towles, Joseph A. Bank, 2014, SC14: International Conference for High Performance Computing, Networking, Storage and Analysis.

A bayesian approach to transcript estimation from gene array data: the BEAM technique

Ron O. Dror, Jonathan G. Murnick, Voichita D. Marinescu, 2002, RECOMB '02.

9.6 New Technologies for Molecular Dynamics Simulations

John L. Klepeis, David E. Shaw, Ron O. Dror, 2012 .

Overview of neutral territory methods for the parallel evaluation of pairwise particle interactions

David E. Shaw, Ron O. Dror, Kevin J. Bowers, 2005 .

A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton

J. P. Grossman, Joseph A. Bank, David E. Shaw, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Equivariant Graph Neural Networks for 3D Macromolecular Structure pdf

Ron O. Dror, Stephan Eismann, Bowen Jing, 2021, ArXiv.

ARES-specific adaptation of E3NN

Andrew M. Watkins, Ron O. Dror, Stephan Eismann, 2021 .

ATOM3D: Protein Structure Ranking (PSR) Dataset

Russ B. Altman, Ron O. Dror, Risi Kondor, 2021 .

Geometric Deep Learning on Biomolecular Structure

Ron O. Dror, Raphael J. L. Townshend, Ligia Melo, 2021 .

Training code for ARES neural network

Andrew M. Watkins, Ron O. Dror, Rhiju Das, 2021 .

ATOM3D: RNA Structure Ranking (RSR) Dataset

Russ B. Altman, Ron O. Dror, Risi Kondor, 2021 .

Anton 3: twenty microseconds of molecular dynamics simulation before lunch

Andrew G. Taube, John L. Klepeis, J. P. Grossman, 2021, SC.

Molecular Dynamics Simulation for All

Ron O. Dror, R. Dror, S. Hollingsworth, 2018, Neuron.

Structural basis for nucleotide exchange in heterotrimeric G proteins

Ron O. Dror, Aashish Manglik, Brian K. Kobilka, 2015, Science.

Structural basis for chemokine recognition and activation of a viral G protein–coupled receptor

A. J. Venkatakrishnan, Ron O. Dror, John S. Burg, 2014, Science.

Identification Of Two Distinct Inactive Conformations Of The Beta-2 Adrenergic Receptor Reconciles Structural And Biochemical Observations

Ron O. Dror, David W. Borhani, David E. Shaw, 2009 .

Publisher's Note: Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations [Phys. Rev. E80, 046705 (2009)]

Ron O. Dror, Huafeng Xu, Michael P. Eastwood, 2009 .

Structure and Function of an Irreversible Agonist-β2 Adrenoceptor complex

Cheng Zhang, Ron O. Dror, Brian K. Kobilka, 2010, Nature.

Diverse GPCRs exhibit conserved water networks for stabilization and activation

A. J. Venkatakrishnan, Ron O. Dror, Brian K. Kobilka, 2019, Proceedings of the National Academy of Sciences.

Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor

Ron O. Dror, Naomi R. Latorraca, Stephan Eismann, 2020, Science.

Structural mechanisms of selectivity and gating in anion channelrhodopsins

Hideki Kandori, Ron O. Dror, Brian K. Kobilka, 2018, Nature.

Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations

Ron O. Dror, Brian K. Kobilka, Naomi R. Latorraca, 2019, Cell.

Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket

Ron O. Dror, Stephen C. Blacklow, Brendan Kelly, 2016, Cell.

Geometric deep learning of RNA structure

Andrew M. Watkins, Ron O. Dror, Rhiju Das, 2021, Science.

Structure of a Signaling Cannabinoid Receptor 1-G Protein Complex

Ron O. Dror, Brian K. Kobilka, Naomi R. Latorraca, 2019, Cell.

Uncovering patterns of atomic interactions in static and dynamic structures of proteins

A. J. Venkatakrishnan, M. Madan Babu, Ron O. Dror, 2019, bioRxiv.

Noise Models in Gene Array Analysis

Ron O. Dror, R. Dror, 2001 .

Estimating Surface Reflectance from Images

Edward H. Adelson, Ron O. Dror, 2001 .

Perspectives on : Molecular dynamics and computational methods Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

Ron O. Dror, Morten Ø. Jensen, David W. Borhani, .

High-resolution Crystal Structure of Human Protease-activated Receptor 1 Bound to the Antagonist Vorapaxar Hhs Public Access

Cheng Zhang, Ron O. Dror, Brian K. Kobilka, 2022 .

Irreversible Agonist-Beta2 Adrenoceptor Complex

Cheng Zhang, Ron O. Dror, Brian K. Kobilka, 2011 .

Anton: A specialized ASIC for molecular dynamics

Ron O. Dror, John K. Salmon, Cliff Young, 2008, 2008 IEEE Hot Chips 20 Symposium (HCS).

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

Ron O. Dror, Morten Ø. Jensen, David W. Borhani, 2010, The Journal of general physiology.

Mechanism of Voltage Gating in Potassium Channels

Ron O. Dror, Morten Ø. Jensen, David W. Borhani, 2012, Science.

High-resolution crystal structure of human Protease-Activated Receptor 1 bound to the antagonist vorapaxar

Ron O. Dror, Brian K. Kobilka, Cheng Zhang, 2012, Nature.

Crystal structure of the natural anion-conducting channelrhodopsin GtACR1

Hideki Kandori, Ron O. Dror, Brian K. Kobilka, 2018, Nature.

Structural insights into μ-opioid receptor activation

Stephen M. Husbands, A. J. Venkatakrishnan, Ron O. Dror, 2015, Nature.

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

Kresten Lindorff-Larsen, Ron O. Dror, John K. Salmon, 2012, PloS one.