D. Shaw

发表

Parallel random numbers: As easy as 1, 2, 3

Mark A. Moraes, Ron O. Dror, David E. Shaw, 2011, 2011 International Conference for High Performance Computing, Networking, Storage and Analysis (SC).

Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, J. A. Bank, R. Dror, 2022 .

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Matthew P. Repasky, J. K. Perry, Daniel T. Mainz, 2004, Journal of medicinal chemistry.

Biomolecular simulation: a computational microscope for molecular biology.

J. P. Grossman, Robert M. Dirks, R. Dror, 2012, Annual review of biophysics.

A hierarchical approach to all‐atom protein loop prediction

B. Honig, R. Friesner, D. Shaw, 2004, Proteins.

Improved side-chain torsion potentials for the Amber ff99SB protein force field

R. Dror, K. Lindorff-Larsen, D. Shaw, 2010, Proteins.

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.

R. Dror, R. Friesner, K. Lindorff-Larsen, 2008, The journal of physical chemistry. B.

Assessment of the utility of contact‐based restraints in accelerating the prediction of protein structure using molecular dynamics simulations

D. Shaw, S. Piana, M. Eastwood, 2015, Protein science : a publication of the Protein Society.

How Fast-Folding Proteins Fold

R. Dror, K. Lindorff-Larsen, D. Shaw, 2011, Science.

Systematic Validation of Protein Force Fields against Experimental Data

R. Dror, K. Lindorff-Larsen, D. Shaw, 2012, PloS one.

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.

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation.

R. Dror, D. Shaw, M. Eastwood, 2005, The Journal of chemical physics.

RNA force field with accuracy comparable to state-of-the-art protein force fields

Robert M. Dirks, D. Shaw, S. Piana, 2018, Proceedings of the National Academy of Sciences.

Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations

Venkatesh Mysore, Yibing Shan, Lijun Liu, 2014, Science Signaling.

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.

Long-timescale molecular dynamics simulations of protein structure and function.

R. Dror, K. Lindorff-Larsen, D. Shaw, 2009, Current opinion in structural biology.

How robust are protein folding simulations with respect to force field parameterization?

K. Lindorff-Larsen, D. Shaw, S. Piana, 2011, Biophysical journal.

Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin

Huafeng Xu, David E. Shaw, D. Shaw, 2020, bioRxiv.

Pathway and mechanism of drug binding to G-protein-coupled receptors

Albert C. Pan, R. Dror, D. Shaw, 2011, Proceedings of the National Academy of Sciences.

Molecular determinants of drug-receptor binding kinetics.

Albert C. Pan, R. Dror, D. Shaw, 2013, Drug discovery today.

The Dynamic Process of β2-Adrenergic Receptor Activation

Albert C. Pan, R. Dror, L. Mueller, 2013, Cell.

Activation mechanism of the β2-adrenergic receptor

Albert C. Pan, R. Dror, D. Shaw, 2011, Proceedings of the National Academy of Sciences.

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations.

Michael P Eastwood, Ron O Dror, Huafeng Xu, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Structural basis of interaction between urokinase-type plasminogen activator and its receptor.

D. Shaw, J. Lubkowski, A. Mazar, 2006, Journal of molecular biology.

Structure and Dynamics of the M3 Muscarinic Acetylcholine Receptor

Albert C. Pan, R. Dror, J. Wess, 2012, Nature.

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin.

K. Lindorff-Larsen, D. Shaw, P. Maragakis, 2016, The journal of physical chemistry. B.

Atomic-level description of ubiquitin folding

K. Lindorff-Larsen, D. Shaw, S. Piana, 2013, Proceedings of the National Academy of Sciences.

Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations.

Albert C. Pan, D. Shaw, Huafeng Xu, 2017, Journal of chemical theory and computation.

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation.

K. Lindorff-Larsen, D. Shaw, P. Maragakis, 2012, Journal of the American Chemical Society.

Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

Paul Robustelli, D. Shaw, S. Piana, 2015, The journal of physical chemistry. B.

Computational design and experimental testing of the fastest-folding β-sheet protein.

M. Gruebele, K. Lindorff-Larsen, D. Shaw, 2011, Journal of molecular biology.

Developing a molecular dynamics force field for both folded and disordered protein states

Paul Robustelli, D. Shaw, S. Piana, 2018, Proceedings of the National Academy of Sciences.

Improving Molecular Mechanics Force Fields By Comparison Of Microsecond Simulations With Nmr Experiments

R. Dror, K. Lindorff-Larsen, D. Shaw, 2009 .

Atomic-level characterization of protein–protein association

Albert C. Pan, Daniel Jacobson, D. Shaw, 2018, Proceedings of the National Academy of Sciences.

Post-Silicon Debug Using Formal Verification Waypoints

J. P. Grossman, Martin M. Deneroff, Stanley C. Wang, 2009 .

Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization

Eric T. Kim, R. Dror, J. Jumper, 2012, Cell.

Transitions to catalytically inactive conformations in EGFR kinase

Albert C. Pan, Eric T. Kim, D. Shaw, 2013, Proceedings of the National Academy of Sciences.

Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor

D. Shaw, Y. Shan, J. Groves, 2013, Cell.

Structure of Human Urokinase Plasminogen Activator in Complex with Its Receptor

D. Shaw, C. Bian, A. Mazar, 2006, Science.

Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine

D. Shaw, 2013 .

Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor

Albert C. Pan, R. Dror, D. Shaw, 2016, Molecular Pharmacology.

A conserved protonation-dependent switch controls drug binding in the Abl kinase

R. Dror, M. Jensen, D. Shaw, 2009, Proceedings of the National Academy of Sciences.

How does a drug molecule find its target binding site?

Eric T. Kim, R. Dror, D. Shaw, 2011, Journal of the American Chemical Society.

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

Albert C. Pan, R. Dror, D. Shaw, 2013, Nature.

Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase

Yibing Shan, Eric T. Kim, S. Hubbard, 2014, Nature Structural &Molecular Biology.

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody

Thomas B. Kepler, Huafeng Xu, Surender Khurana, 2012, Proceedings of the National Academy of Sciences.

Atomic-level simulation of current–voltage relationships in single-file ion channels

Michael P. Eastwood, Morten Ø. Jensen, Vishwanath Jogini, 2013, The Journal of general physiology.

Fragment Hits: What do They Look Like and How do They Bind?

Miklos Feher, Fabrizio Giordanetto, D. Shaw, 2019, Journal of medicinal chemistry.

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein

Paul Robustelli, D. Shaw, S. Piana, 2020, bioRxiv.

Structural origin of slow diffusion in protein folding

William A. Eaton, Stefano Piana-Agostinetti, David E. Shaw, 2015, Science.

Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations

Ron O Dror, R. Dror, M. Jensen, 2009, Proceedings of the National Academy of Sciences.

An anti-urokinase plasminogen activator receptor (uPAR) antibody: crystal structure and binding epitope.

D. Shaw, A. Mazar, Liqing Chen, 2006, Journal of molecular biology.

An anti-urokinase plasminogen activator receptor antibody (ATN-658) blocks prostate cancer invasion, migration, growth, and experimental skeletal metastasis in vitro and in vivo.

D. Shaw, A. Mazar, S. Rabbani, 2010, Neoplasia.

Mechanism of Voltage Gating in Potassium Channels

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

2 . COUNTER-BASED RANDOM NUMBER GENERATION

R. Dror, J. Salmon, M. A. Moraes, 2011 .

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.

Automated Empirical Optimization

Chi-Bang Kuan, Gul Agha, Peter Sanders, 2011, Encyclopedia of Parallel Computing.

Structural basis for nucleotide exchange in heterotrimeric G proteins

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

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

John L. Klepeis, David E. Shaw, Charles A. Rendleman, 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

Anton, a special-purpose machine for molecular dynamics simulation

J. P. Grossman, Martin M. Deneroff, Richard H. Larson, 2008, CACM.

Inhibition of angiogenesis by cleaved high molecular weight kininogen (HKa) and HKa domain 5.

D. Shaw, K. McCrae, F. Doñate, 2005, Current cancer drug targets.

Phase 1 trial of the antiangiogenic peptide ATN-161 (Ac-PHSCN-NH2), a beta integrin antagonist, in patients with solid tumours

D. Shaw, L. Weiner, A. Mazar, 2006, British Journal of Cancer.

Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family

Eric T. Kim, R. Dror, D. Shaw, 2013, eLife.

Millisecond-scale molecular dynamics simulations on Anton

J. P. Grossman, Joseph A. Bank, Martin M. Deneroff, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment.

Albert C. Pan, T. Chitra, J. Jumper, 2013, The journal of physical chemistry. B.

Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule.

Albert C. Pan, R. Dror, D. Shaw, 2015, Biochemistry.

Atomic-level characterization of protein-protein association

Albert C. Pan, Daniel Jacobson, D. Shaw, 2018, bioRxiv.

Exploiting allosteric properties of RAF and MEK inhibitors to target therapy-resistant tumors driven by oncogenic BRAF signaling.

D. Shaw, M. Herlyn, A. Schlessinger, 2021, Cancer discovery.

Ab Initio Molecular Dynamics

Chi-Bang Kuan, Gul Agha, Peter Sanders, 2011, Encyclopedia of Parallel Computing.

Millisecond-scale molecular dynamics simulations on Anton

J. P. Grossman, Joseph A. Bank, Martin M. Deneroff, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Two‐chain high molecular weight kininogen induces endothelial cell apoptosis and inhibits angiogenesis: partial activity within domain 5

D. Shaw, R. Sakthivel, K. Claffey, 2000, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Copper Binding by Tetrathiomolybdate Attenuates Angiogenesis and Tumor Cell Proliferation through the Inhibition of Superoxide Dismutase 1

D. Shaw, A. Mazar, F. Doñate, 2006, Clinical Cancer Research.

Structural mechanism for Bruton’s tyrosine kinase activation at the cell membrane

Albert C. Pan, D. Shaw, Qi Wang, 2018, Proceedings of the National Academy of Sciences.

Identification of biomarkers for the antiangiogenic and antitumour activity of the superoxide dismutase 1 (SOD1) inhibitor tetrathiomolybdate (ATN-224)

D. Shaw, A. Mazar, F. Doñate, 2008, British Journal of Cancer.

Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA–Protein Complexes

Michael V. LeVine, D. Shaw, S. Piana, 2022, The journal of physical chemistry. B.

Cancer Therapy: Preclinical Targeting the Urokinase Plasminogen Activator Receptor Inhibits Ovarian Cancer Metastasis

H. Im, D. Shaw, E. Lengyel, 2011 .

Peptides Derived from the Histidine-Proline Domain of the Histidine-Proline-Rich Glycoprotein Bind to Tropomyosin and Have Antiangiogenic and Antitumor Activities

D. Shaw, A. Mazar, F. Doñate, 2004, Cancer Research.

Anton, a special-purpose machine for molecular dynamics simulation

J. P. Grossman, Martin M. Deneroff, Richard H. Larson, 2008, CACM.

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 .

Anton: A specialized ASIC for molecular dynamics

Ron O. Dror, John K. Salmon, Cliff Young, 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.

A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions

David E. Shaw, D. Shaw, 2005, J. Comput. Chem..

Mechanism of NMDA receptor channel block by MK-801 and memantine

David E. Shaw, Hassane S. Mchaourab, Richard A. Stein, 2018, Nature.

Synthesis and evaluation of multisubstrate bicyclic pyrimidine nucleoside inhibitors of human thymidine phosphorylase.

B. Ganem, D. Shaw, Weiru Wang, 2006, Journal of medicinal chemistry.

Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

Federico D. Sacerdoti, Brent A. Gregersen, Mark A. Moraes, 2006, ACM/IEEE SC 2006 Conference (SC'06).

PNAS201713027 1..10

Robert M. Dirks, D. Shaw, S. Piana, 2018 .

Structural basis for backtracking by the SARS-CoV-2 replication–transcription complex

B. Chait, D. Shaw, E. Eng, 2021, Proceedings of the National Academy of Sciences.

Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex

B. Chait, D. Shaw, E. Eng, 2021, bioRxiv.

Anton, a special-purpose machine for molecular dynamics simulation

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

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

David E. Shaw, Richard A. Friesner, Steven L. Dixon, 2006, J. Comput. Aided Mol. Des..

9.6 New Technologies for Molecular Dynamics Simulations

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

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..

The midpoint method for parallelization of particle simulations.

Ron O Dror, R. Dror, K. Bowers, 2006, The Journal of chemical physics.

The role of ligands on the equilibria between functional states of a G protein-coupled receptor.

R. Dror, D. Shaw, K. Chung, 2013, Journal of the American Chemical Society.

Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization

D. Shaw, Y. Shan, A. Hata, 2021, Nature Communications.

Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens

R. Dror, M. Jensen, D. Shaw, 2008, Proceedings of the National Academy of Sciences.

Suppressing Kv1.3 Ion Channel Activity with a Novel Small Molecule Inhibitor Ameliorates Inflammation in a Humanised Mouse Model of Ulcerative Colitis

M. Jensen, D. Shaw, A. Aszódi, 2021, Journal of Crohn's & colitis.

Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3

John Kuriyan, Yibing Shan, D. Shaw, 2009, Proceedings of the National Academy of Sciences.

Angiogenesis blockade as a new therapeutic approach to experimental colitis

D. Shaw, C. A. de la Motte, A. Levine, 2006, Gut.

EGFR oligomerization organizes kinase-active dimers into competent signalling platforms

Anton Arkhipov, Martyn D Winn, Alireza Lajevardipour, 2016, Nature Communications.

Targetable HER3 functions driving tumorigenic signaling in HER2-amplified cancers

D. Shaw, Y. Shan, M. Moasser, 2022, Cell reports.

A non–RGD-based integrin binding peptide (ATN-161) blocks breast cancer growth and metastasis in vivo

D. Shaw, A. Mazar, G. Parry, 2006, Molecular Cancer Therapeutics.

IRAK4 dimerization and trans-autophosphorylation are induced by Myddosome assembly.

Hao Wu, D. Shaw, Y. Shan, 2014, Molecular cell.

Identifying localized changes in large systems: Change-point detection for biomolecular simulations

Stefano Piana, Ron O Dror, David E Shaw, 2015, Proceedings of the National Academy of Sciences.

Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations.

John Kuriyan, Yibing Shan, Dustin J Maly, 2009, Cancer research.

Mechanism of Na+/H+ Antiporting

Brent A. Gregersen, R. Dror, K. Bowers, 2007, Science.

A dynamically coupled allosteric network underlies binding cooperativity in Src kinase

Yibing Shan, Eric T. Kim, David E. Shaw, 2015, Nature Communications.

Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor

David E. Shaw, Anton Arkhipov, Yibing Shan, 2014, PLoS Comput. Biol..

Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication–transcription complex

D. Shaw, E. Eng, S. Darst, 2022, Nature Structural & Molecular Biology.

Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex

D. Shaw, E. Eng, S. Darst, 2021, bioRxiv.

A structural model of a Ras–Raf signalosome

P. Jänne, D. Shaw, Y. Shan, 2020, Nature Structural & Molecular Biology.

Preliminary characterization of ribosomes of Entamoeba invadens.

D. Shaw, D. Weller, R. Boudreau, 1983, Molecular and biochemical parasitology.

Architecture and Membrane Interactions of the EGF Receptor

Anton Arkhipov, John Kuriyan, Yibing Shan, 2013, Cell.

The role of Cascade, a cycle-based simulation infrastructure, in designing the Anton special-purpose supercomputers

J. P. Grossman, Brian Towles, Joseph A. Bank, 2013, 2013 50th ACM/EDAC/IEEE Design Automation Conference (DAC).

Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes

D. Shaw, Aiwu Zhou, A. Mazar, 2008, Nature Structural &Molecular Biology.

How IGF-1 activates its receptor

D. Shaw, Y. Shan, K. Hristova, 2014, eLife.

Assessing the Accuracy of Two Enhanced Sampling Methods Using EGFR Kinase Transition Pathways: The Influence of Collective Variable Choice.

David E Shaw, Albert C Pan, Thomas M Weinreich, 2014, Journal of chemical theory and computation.

Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication–transcription complex

D. Shaw, E. Eng, S. Darst, 2022, Nature Structural & Molecular Biology.

Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS)

E. L. Guenther, Albert C. Pan, D. Eisenberg, 2017, Proceedings of the National Academy of Sciences.

AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets

Miklos Feher, David E Shaw, Brian Cole, 2020, J. Chem. Inf. Model..

Structure and Function of an Irreversible Agonist-β2 Adrenoceptor complex

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

Targeting the Urokinase Plasminogen Activator Receptor Inhibits Ovarian Cancer Metastasis

H. Im, D. Shaw, E. Lengyel, 2010, Clinical Cancer Research.

Structural basis of AZD9291 selectivity for EGFR T790M.

D. Shaw, Y. Shan, H. Choi, 2020, Journal of medicinal chemistry.

Regulation of RAS oncogenicity by acetylation

Eric T. Kim, D. Shaw, Y. Shan, 2012, Proceedings of the National Academy of Sciences.

Structural models of full-length JAK2 kinase

S. Hubbard, D. Shaw, Y. Shan, 2019, bioRxiv.

Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage

Huafeng Xu, Hua-Xin Liao, Thomas B Kepler, 2015, Proteins.

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein.

Paul Robustelli, D. Shaw, S. Piana, 2020, Journal of the American Chemical Society.

Histidine-Proline Rich Glycoprotein (HPRG) binds and transduces anti-angiogenic signals through cell surface tropomyosin on endothelial cells

D. Shaw, A. Mazar, K. McCrae, 2004, Thrombosis and Haemostasis.

The u-series: A separable decomposition for electrostatics computation with improved accuracy.

J. P. Grossman, Robert M. Dirks, Adam K. Lerer, 2019, The Journal of chemical physics.

Histidine-proline-rich glycoprotein has potent antiangiogenic activity mediated through the histidine-proline-rich domain.

D. Shaw, A. Mazar, G. Parry, 2002, Cancer research.

Pharmacology of the Novel Antiangiogenic Peptide ATN-161 (Ac-PHSCN-NH2): Observation of a U-Shaped Dose-Response Curve in Several Preclinical Models of Angiogenesis and Tumor Growth

D. Shaw, R. Kerbel, Y. Shaked, 2008, Clinical Cancer Research.

Crystal structures of the Jak2 pseudokinase domain and the pathogenic mutant V617F

Yibing Shan, Stevan R. Hubbard, David E. Shaw, 2012, Nature Structural &Molecular Biology.

Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations

Stefano Piana, Alpan Raval, Michael P Eastwood, 2012, Proteins.

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.

A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis

D. Shaw, P. Maragakis, J. Izaguirre, 2020, bioRxiv.

Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography

Hunter M Nisonoff, Hunter M. Nisonoff, D. Shaw, 2023, bioRxiv.

Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist

R. Dror, D. Shaw, Y. Zou, 2018, Nature Chemical Biology.

Superoxide dismutase 1 (SOD1) is essential for H2O2-mediated oxidation and inactivation of phosphatases in growth factor signaling

D. Shaw, A. Mazar, N. Tonks, 2008, Proceedings of the National Academy of Sciences.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks.

Andrew G. Taube, Robert T McGibbon, Karthik Siva, 2017, The Journal of chemical physics.

The future of molecular dynamics simulations in drug discovery

David E. Shaw, David W. Borhani, D. Shaw, 2011, Journal of Computer-Aided Molecular Design.

Atomic-Level Description of Protein Folding inside the GroEL Cavity.

D. Shaw, S. Piana, 2018, The journal of physical chemistry. B.

Quantum chemical benchmark databases of gold-standard dimer interaction energies

Andrew G. Taube, Brent A. Gregersen, R. McGibbon, 2021, Scientific data.

The Specialized High-Performance Network on Anton 3

J. P. Grossman, Brian Towles, Keun Sup Shim, 2022, 2022 IEEE International Symposium on High-Performance Computer Architecture (HPCA).

Protein folding kinetics and thermodynamics from atomistic simulation

Kresten Lindorff-Larsen, K. Lindorff-Larsen, D. Shaw, 2012, Proceedings of the National Academy of Sciences.

How does a small molecule bind at a cryptic binding site?

Eric T. Kim, D. Shaw, Y. Shan, 2021, bioRxiv.

Midtown splines: An optimal charge assignment for electrostatics calculations.

David E Shaw, Cristian Predescu, Michael Bergdorf, 2020, The Journal of chemical physics.

Principles of conduction and hydrophobic gating in K+ channels

Kresten Lindorff-Larsen, Michael P Eastwood, Ron O Dror, 2010, Proceedings of the National Academy of Sciences.

Anton 3: Twenty Microseconds of Molecular Dynamics Simulation Before Lunch

Andrew G. Taube, J. P. Grossman, Joseph A. Bank, 2021, SC21: International Conference for High Performance Computing, Networking, Storage and Analysis.

166 Millisecond-long molecular dynamics simulations of proteins on a special-purpose machine

David E. Shaw, D. Shaw, 2013 .

Gating and modulation of an inward-rectifier potassium channel

M. Jensen, D. Shaw, V. Jogini, 2022, The Journal of general physiology.

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure.

Kenneth M. Mackenzie, R. Dror, R. Lippert, 2013, The Journal of chemical physics.

Mechanism of NMDA receptor channel block by MK-801 and memantine

E. Gouaux, M. Jensen, D. Shaw, 2018, Nature.

Efficient hyperparameter optimization by way of PAC-Bayes bound minimization pdf

John J. Cherian, Andrew G. Taube, R. McGibbon, 2020, ArXiv.

A Simple Model of Multivalent Adhesion and Its Application to Influenza Infection

D. Shaw, Huafeng Xu, 2016, Biophysical journal.

Desmond Performance on a Cluster of Multicore Processors

Edmond Chow, David E. Shaw, Federico D. Sacerdoti, 2008 .

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.

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.

Stefano Piana, David E Shaw, Albert C Pan, 2016, Journal of chemical theory and computation.

Molecular Basis of Small-Molecule Binding to α-Synuclein

Albert C. Pan, Paul Robustelli, D. Shaw, 2021, bioRxiv.

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.

Stefano Piana, David E Shaw, John L Klepeis, 2014, Current opinion in structural biology.

Atomistic description of the folding of a dimeric protein.

Kresten Lindorff-Larsen, K. Lindorff-Larsen, D. Shaw, 2013, The journal of physical chemistry. B.

Development of a force field for the simulation of single-chain proteins and protein-protein complexes.

Paul Robustelli, D. Shaw, S. Piana, 2020, Journal of chemical theory and computation.

Structural mechanism of a drug-binding process involving a large conformational change of the protein target

D. Shaw, Y. Shan, M. Seeliger, 2023, Nature Communications.

A deep-learning view of chemical space designed to facilitate drug discovery

David E. Shaw, Brian Cole, Hunter M. Nisonoff, 2020, J. Chem. Inf. Model..

Desensitization dynamics of the AMPA receptor.

Albert C. Pan, M. Jensen, D. Shaw, 2023, Structure.

Correction to How Does a Drug Molecule Find its Target Binding Site

Eric T. Kim, R. Dror, D. Shaw, 2014 .

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.

Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations.

David E Shaw, Robert M. Dirks, Huafeng Xu, 2012, Journal of chemical theory and computation.

Allosteric activation of apicomplexan calcium-dependent protein kinases

D. Shaw, Y. Shan, H. Ploegh, 2015, Proceedings of the National Academy of Sciences.

Computationally efficient molecular dynamics integrators with improved sampling accuracy

David E. Shaw, Huafeng Xu, Kevin J. Bowers, 2012 .

The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers

Laura C. Zanetti-Domingues, D. Shaw, Y. Shan, 2018, Nature Communications.

A common, avoidable source of error in molecular dynamics integrators.

Michael P Eastwood, Ron O Dror, Istvan Kolossvary, 2007, The Journal of chemical physics.

RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations.

D. Bergstrom, D. Shaw, A. Schram, 2023, Cancer discovery.

Abstract 3327: Discovery and characterization of the potent, allosteric SHP2 inhibitor GDC-1971 for the treatment of RTK/RAS driven tumors

D. Bergstrom, M. Murcko, D. Shaw, 2022, Cancer Research.

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

Kresten Lindorff-Larsen, Victor Muñoz, Clara M. Santiveri, 2015, Journal of the American Chemical Society.

Desmond/GPU Performance as of November 2014

Michael Bergdorf, David E. Shaw, Charles A. Rendleman, 2014 .

Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography

Hunter M. Nisonoff, D. Shaw, P. Maragakis, 2023, J. Chem. Inf. Model..

High-resolution crystal structure of human protease-activated receptor 1

R. Dror, D. Shaw, W. Weis, 2012, Nature.

Atomic-Level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, J. A. Bank, R. Dror, 2010, Science.

Filtering, Reductions and Synchronization in the Anton 2 Network

J. P. Grossman, Brian Towles, David E. Shaw, 2015, 2015 IEEE International Parallel and Distributed Processing Symposium.

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

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

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.

Stefano Piana, Willy Wriggers, Michael P Eastwood, 2009, Journal of chemical theory and computation.

Accelerating Parallel Analysis of Scientific Simulation Data via Zazen

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

Structure of the M3 Muscarinic Acetylcholine Receptor

Albert C. Pan, R. Dror, J. Wess, 2012 .

Extracellular tropomyosin: a novel common pathway target for anti-angiogenic therapy.

D. Shaw, A. Mazar, K. McCrae, 2004, Current cancer drug targets.

Atomic-Level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, R. Dror, J. Salmon, 2010, Science.

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

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

The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers

Laura C. Zanetti-Domingues, D. Shaw, F. Gervasio, 2018, Nature Communications.

Unifying on-chip and inter-node switching within the Anton 2 network

J. P. Grossman, Brian Towles, David E. Shaw, 2014, 2014 ACM/IEEE 41st International Symposium on Computer Architecture (ISCA).

Equipartition and the Calculation of Temperature in Biomolecular Simulations.

Michael P Eastwood, Ron O Dror, Kate A. Stafford, 2010, Journal of chemical theory and computation.

Allosteric activation of apicomplexan calcium-dependent protein kinases

D. Shaw, H. Ploegh, T. Schwartz, 2015, Proceedings of the National Academy of Sciences.

Atomistic description of the folding of a dimeric protein.

K. Lindorff-Larsen, D. Shaw, S. Piana, 2013, The journal of physical chemistry. B.

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

Robert M. Dirks, R. Dror, J. Salmon, 2012, PloS one.

Pharmacology of the Novel Antiangiogenic Peptide ATN-161 (Ac-PHSCN-NH2): Observation of a U-Shaped Dose-Response Curve in Several Preclinical Models of Angiogenesis and Tumor Growth

D. Shaw, R. Kerbel, Y. Shaked, 2008, Clinical Cancer Research.

Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor

D. Shaw, J. Groves, J. Kuriyan, 2013, Cell.

Mechanism of Voltage Gating in Potassium Channels

R. Dror, M. Jensen, D. Shaw, 2012, 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 .

ATLAS (Automatically Tuned Linear Algebra Software)

R. C. Whaley, R. Clint Whaley, Rajesh K. Karmani, 2011, Encyclopedia of Parallel Computing.

Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment.

Albert C. Pan, J. Jumper, D. Shaw, 2013, The journal of physical chemistry. B.

Algorithmic Skeletons

Rajesh K. Karmani, R. Tuminaro, P. Sanders, 2011, Encyclopedia of Parallel Computing.

Times Square sampling: an adaptive algorithm for free energy estimation

Michael Snarski, Avi Robinson-Mosher, Duluxan Sritharan, 2021, Journal of Computational and Graphical Statistics.

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.

Anton: A Specialized Machine for Millisecond-Scale Molecular Dynamics Simulations of Proteins

David E. Shaw, D. Shaw, 2009, 2009 19th IEEE Symposium on Computer Arithmetic.