W. Huang, A. Manglik, A.J. Venkatakrishnan, T. Laeremans, E.N. Feinberg, A.L. Sanborn, H. Kato, K.E. Livingston, T.S. Thorsen, R. Kling, S. Granier, P. Gmeiner, S.M. Husbands, J.R. Traynor, W.I. Weis, J. Steyaert, R.O. Dror, and B.K. Kobilka. Structural insights into μ-opioid receptor activation. Nature. In press

R.O. Dror, T.J. Mildorf, D. Hilger, A. Manglik, D.W. Borhani, D.H. Arlow, A. Philippsen, N. Villanueva, Z. Yang, M. Lerch, W.L. Hubbell, B.K. Kobilka, R.K. Sunahara, and D.E. Shaw. Structural basis for nucleotide exchange in heterotrimeric G proteins. Science 348: 1361-1365 (2015)

J.S. Burg, J.R. Ingram, A.J. Venkatakrishnan, K.M. Jude, A. Dukkipati, E.N. Feinberg, A. Angelini, D. Waghray, R.O. Dror, H.L. Ploegh, and K.C. Garcia. Structural basis for chemokine recognition and activation of a viral G protein–coupled receptor. Science 347: 1113-1117 (2015)

Z. Fan, R.O. Dror, T.J. Mildorf, S. Piana, and D.E. Shaw. Identifying localized changes in large systems: change-point detection for biomolecular simulations. Proceedings of the National Academy of Sciences of the United States of America 112: 7454-7459 (2015)

A. Ranganathan, R.O. Dror, J. Carlsson. Insights into the role of Asp79^2.50 in β₂ adrenergic receptor activation from molecular dynamics simulations. Biochemistry 53: 7283-7296 (2014)

D.E. Shaw, J.P. Grossman, J.A. Bank, B. Batson, J.A. Butts, J.C. Chao, M.M. Deneroff, R.O. Dror, A. Even, C.H. Fenton, A. Forte, J. Gagliardo, G. Gill, B. Greskamp, C.R. Ho, D.J. Ierardi, L. Iserovich, J.S. Kuskin, R.H. Larson, T. Layman, L.-S. Lee, A.K. Lerer, C. Li, D. Killebrew, K.M. Mackenzie, Shark Y.-H. Mok, M.A. Moraes, R. Mueller, L.J. Nociolo, J.L. Peticolas, T. Quan, D. Ramot, J.K. Salmon, D.P. Scarpazza, U.B. Schafer, N. Siddique, C.W. Snyder, J. Spengler, P.T.P. Tang, M. Theobald, H. Toma, B. Towles, B. Vitale, S.C. Wang, and C. Young. Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC14). Piscataway, NJ: IEEE. 41–53 (2014). Gordon Bell Prize.

R.O. Dror, H.F. Green, C. Valant, D.W. Borhani, J.R. Valcourt, A.C. Pan, D.H. Arlow, M. Canals, J.R. Lane, R. Rahmani, J.B. Baell, P.M. Sexton, A. Christopoulos, and D.E. Shaw. Structural basis for modulation of a GPCR by allosteric drugs. Nature 503:295-299 (2013)

R. Nygaard, Y. Zou, R.O. Dror, T.J. Mildorf, D.H. Arlow, A. Manglik, A.C. Pan, C.W. Liu, J.J. Fung, M.P. Bokoch, F.S. Thian, T.S. Kobilka, D.E. Shaw, L. Mueller, R.S. Prosser, and B.K. Kobilka. The dynamic process of β₂-adrenergic receptor activation. Cell 152:532-542 (2013)

A.C. Pan, D.W. Borhani, R.O. Dror, and D.E. Shaw. Molecular determinants of drug–receptor binding kinetics. Drug Discovery Today 18:667-673 (2013)

D.P. Scarpazza, D.J. Ierardi, A.K. Lerer, K. M. Mackenzie, A.C. Pan, J.A. Bank, E. Chow, R.O. Dror, J.P. Grossman, D. Killebrew, M.A. Moraes, C. Predescu, J.K. Salmon, and D.E. Shaw. Extending the generality of molecular dynamics simulations on a special-purpose machine. Proceedings of the 27th IEEE International Parallel and Distributed Processing Symposium (IPDPS). Boston, MA: IEEE Computer Society. 933-945 (2013). Best Paper Award (Applications Track).

J.P. Grossman, J.S. Kuskin, J.A. Bank, M. Theobald, R.O. Dror, D.J. Ierardi, R.H. Larson, U.B. Schafer, B. Towles, C. Young, and D.E. Shaw. Hardware support for fine-grained event-driven computation in Anton 2. Proceedings of the Eighteenth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS). New York, NY: ACM. 549-560 (2013)

A. Arkhipov, Y. Shan, E.T. Kim, R.O. Dror, and D.E. Shaw. Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family. eLife 2:e00708 (2013)

R.A. Lippert, C. Predescu, D.J. Ierardi, K.M. Mackenzie, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure. Journal of Chemical Physics 139:164106 (2013)

T.H. Kim, K.Y. Chung, A. Manglik, A.L. Hansen, R.O. Dror, T.J. Mildorf, D.E. Shaw, B.K. Kobilka, and R.S. Prosser. The role of ligands on the equilibria between functional states of a G protein-coupled receptor. Journal of the American Chemical Society 135:9465-9474 (2013)

C. Zhang, Y. Srinivasan, D.H. Arlow, J.J. Fung, D. Palmer, Y. Zheng, H.F. Green, A. Pandey, R.O. Dror, D.E. Shaw, W.I. Weis, S.R. Coughlin, and B.K. Kobilka. High-resolution crystal structure of human protease-activated receptor 1. Nature 492:387-392 (2012)

R.O. Dror, R.M. Dirks, J.P. Grossman, H. Xu, and D.E. Shaw. Biomolecular simulation: a computational microscope for molecular biology. Annual Review of Biophysics 41:429-452 (2012)

M.Ø. Jensen, V. Jogini, D.W. Borhani, A.E. Leffler, R.O. Dror, and D.E. Shaw. Mechanism of voltage gating in potassium channels. Science 336:229-233 (2012)

Y. Shan, M.P. Eastwood, X. Zhang, E.T. Kim, A. Arkhipov, R.O. Dror, J. Jumper, J. Kuriyan, and D.E. Shaw. Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell 149:860-870 (2012)

A.C. Kruse, J. Hu, A.C. Pan, D.H. Arlow, D.M. Rosenbaum, E. Rosemond, H.F. Green, T. Liu, P.S. Chae, R.O. Dror, D.E. Shaw, W.I. Weis, J. Wess, and B.K. Kobilka. Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature 482:552-556 (2012)

C. Predescu, R.A. Lippert, M.P. Eastwood, D.J. Ierardi, H. Xu, M.Ø. Jensen, K.J. Bowers, J. Gullingsrud, C.A. Rendleman, R.O. Dror, and D.E. Shaw. Computationally efficient molecular dynamics integrators with improved sampling accuracy. Molecular Physics 110:967-983 (2012)

A. Raval, S. Piana, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics 80:2071-2079 (2012)

K. Lindorff-Larsen, P. Maragakis, S. Piana, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Systematic validation of protein force fields against experimental data. PLoS ONE 7:e32131 (2012)

S. Piana, K. Lindorff-Larsen, R.M. Dirks, J.K. Salmon, R.O. Dror, and D.E. Shaw. Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. PLoS ONE 7: e39918 (2012)

R.O. Dror, D.H. Arlow, P. Maragakis, T.J. Mildorf, A.C. Pan, H. Xu, D.W. Borhani, and D.E. Shaw. Activation mechanism of the β₂-adrenergic receptor. Proceedings of the National Academy of Sciences of the USA. 108:18684-18689 (2011)

K. Lindorff-Larsen, S. Piana, R.O. Dror, and D.E. Shaw. How fast-folding proteins fold. Science 334:517-520 (2011)

R.O. Dror, A.C. Pan, D.H. Arlow, D.W. Borhani, P. Maragakis, Y. Shan, H. Xu, and D.E. Shaw. Pathway and mechanism of drug binding to G-protein-coupled receptors. Proceedings of the National Academy of Sciences of the USA. 108:13118-13123 (2011)

D.M. Rosenbaum, C. Zhang, J.A. Lyons, R. Holl, D. Aragao, D.H. Arlow, S.G.F. Rasmussen, H.-J. Choi, B.T. DeVree, R.K. Sunahara, P.S. Chae, S.H. Gellman, R.O. Dror, D.E. Shaw, W.I. Weis, M. Caffrey, P. Gmeiner and B.K. Kobilka. Structure and function of an irreversible agonist-β₂ adrenoceptor complex. Nature 469:236-240 (2011)

J.K. Salmon, M.A. Moraes, R.O. Dror, and D.E. Shaw. Parallel random numbers: as easy as 1, 2, 3. Proceedings of the Conference for High Performance Computing, Networking, Storage and Analysis (SC11). Seattle, Washington (2011). Best Paper Award.

Y. Shan, E.T. Kim, M.P. Eastwood, R.O. Dror, M.A. Seeliger, and D.E. Shaw. How does a drug molecule find its target binding site? Journal of the American Chemical Society 133:9181-9183 (2011)

R.O. Dror, J.P. Grossman, K.M. Mackenzie, B. Towles, E. Chow, J.K. Salmon, C. Young, J.A. Bank, B. Batson, M.M. Deneroff, J.S. Kuskin, R.H. Larson, M.A. Moraes, and D.E. Shaw. Overcoming communication latency barriers in massively parallel scientific computation. IEEE Micro 31:8-19 (2011)

R.O. Dror, C. Young, and D.E. Shaw. Anton: A special-purpose molecular simulation machine. In Encyclopedia of Parallel Computing, D. Padua, ed., New York, NY: Springer (2011)

R.O. Dror, A.C. Pan, D.H. Arlow, and D.E. Shaw. Probing the conformational dynamics of GPCRs with molecular dynamics simulation. In G Protein-Coupled Receptors: From Structure to Function. J. Giraldo and J.-P. Pin, eds. London: Royal Society of Chemistry, 384-400 (2011)

J.A. Butts, P.T.P. Tang, R.O. Dror, and D.E. Shaw. Radix-8 digit-by-rounding: achieving high-performance reciprocals, square roots, and reciprocal square roots. Proceedings of the 20th IEEE Symposium on Computer Arithmetic (ARITH20). Tuebingen, Germany (2011)

P.T.P. Tang, J.A. Butts, R.O. Dror, and D.E. Shaw. Tight certification techniques for digit-by-rounding algorithms with application to a new 1/√x design. Proceedings of the 20th IEEE Symposium on Computer Arithmetic (ARITH20). Tuebingen, Germany (2011)

D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, M.P. Eastwood, J.A. Bank, J.M. Jumper, J.K. Salmon, Y. Shan, and W. Wriggers. Atomic-level characterization of the structural dynamics of proteins. Science 330:341-346 (2010)

R.O. Dror, J.P. Grossman, K.M. Mackenzie, B. Towles, E. Chow, J.K. Salmon, C. Young, J.A. Bank, B. Batson, M.M. Deneroff, J.S. Kuskin, R.H. Larson, M.A. Moraes, and D.E. Shaw, Exploiting 162-nanosecond end-to-end communication latency on Anton, Proceedings of the Conference for High Performance Computing, Networking, Storage and Analysis (SC10) , New Orleans, Louisiana (2010). Best Paper Award Finalist.

R.O. Dror, M.Ø. Jensen, D.W. Borhani, and D.E. Shaw. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. The Journal of General Physiology 135:555-562 (2010)

M.Ø. Jensen, D.W. Borhani, K. Lindorff-Larsen, P. Maragakis, V. Jogini, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Principles of conduction and hydrophobic gating in K⁺ channels. Proceedings of the National Academy of Sciences of the USA 107:5833-5838 (2010)

M.P. Eastwood, K.A. Stafford, R.A. Lippert, M.Ø. Jensen, P. Maragakis, C. Predescu, R.O. Dror, and D.E. Shaw. Equipartition and the calculation of temperature in biomolecular simulations. Journal of Chemical Theory and Computation 6:2045-2058 (2010)

K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror, and D.E. Shaw. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics 78:1950-1958 (2010)

T. Tu, C.A. Rendleman, P.J. Miller, F. Sacerdoti, R.O. Dror, and D.E. Shaw. Accelerating parallel analysis of scientific simulation data via Zazen. Proceedings of the 8th USENIX Conference on File and Storage Technologies (FAST '10), San Jose, California (2010)

K.J. Bowers, R.A. Lippert, R.O. Dror, and D.E. Shaw. Improved twiddle access for fast Fourier transforms. IEEE Transactions on Signal Processing 58:1122-1130 (2010)

R.O. Dror, D.H. Arlow, D.W. Borhani, M.Ø. Jensen, S. Piana, and D.E. Shaw. Identification of two distinct inactive conformations of the β₂-adrenergic receptor reconciles structural and biochemical observations. Proceedings of the National Academy of Sciences of the USA 106:4689-4694 (2009)

D.E. Shaw, R.O. Dror, J.K. Salmon, J.P. Grossman, K.M. Mackenzie, J.A. Bank, C. Young, M.M. Deneroff, B. Batson, K.J. Bowers, E. Chow, M.P. Eastwood, D.J. Ierardi, J.L. Klepeis, J.S. Kuskin, R.H. Larson, K. Lindorff-Larsen, P. Maragakis, M.A. Moraes, S. Piana, Y. Shan, and B. Towles. Millisecond-scale molecular dynamics simulations on Anton Proceedings of the ACM/IEEE Conference on Supercomputing (SC09), Portland, Oregon (2009). Best Paper Award. Gordon Bell Award.

C. Young, J.A. Bank, R.O. Dror, J.P. Grossman, J.K. Salmon, and D.E. Shaw. A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton. Proceedings of the ACM/IEEE Conference on Supercomputing (SC09), Portland, Oregon (2009)

R.O. Dror, M.Ø. Jensen, and D.E. Shaw. Elucidating membrane protein function through long-timescale molecular dynamics simulation. Proceedings of the IEEE Engineering in Medicine and Biology Society Conference (EMBC), Minneapolis, Minnesota (2009)

W. Wriggers, K.A. Stafford, Y. Shan, S. Piana, P. Maragakis, K. Lindorff-Larsen, P.J. Miller, J. Gullingsrud, C.A. Rendleman, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Automated event detection and activity monitoring in long molecular dynamics simulations. Journal of Chemical Theory and Computation 5:2595-2605 (2009)

D.K. Shenfeld, H. Xu, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations. Physical Review E 80:046705 (2009)

Y. Shan, M.A. Seeliger, M.P. Eastwood, F. Frank, H. Xu, M.Ø. Jensen, R.O. Dror, J. Kuriyan, and D.E. Shaw. A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proceedings of the National Academy of Sciences of the United States of America . 106:139-144 (2009)

C.R. Ho, M. Theobald, B. Batson, J.P. Grossman, S.C. Wang, J. Gagliardo, M.M. Deneroff, R.O. Dror, and D.E. Shaw. Post-silicon debug using formal verification waypoints. Proceedings of the Design and Verification Conference and Exhibition (DVCon '09), San Jose, California (2009)

J.L. Klepeis, K. Lindorff-Larsen, R.O. Dror, and D.E. Shaw. Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology, 19:1-18 (2009)

M.Ø. Jensen, R.O. Dror, H. Xu, D.W. Borhani, I.T. Arkin, M.P. Eastwood, and D.E. Shaw. Dynamic Control of Slow Water Transport by Aquaporin 0: Implications for Hydration and Junction Stability in the Eye Lens. Proceedings of the National Academy of Sciences of the USA 105:14430-14435 (2008)

T. Tu, C.A. Rendleman, D.W. Borhani, R.O. Dror, J. Gullingsrud, M.Ø. Jensen, J.L. Klepeis, P. Maragakis, P. Miller, K.A. Stafford, and D.E. Shaw. A Scalable Parallel Framework for Analyzing Terascale Molecular Dynamics Simulation Trajectories. Proceedings of the ACM/IEEE Conference on Supercomputing (SC08), Austin, Texas (2008). Best Paper Award Finalist.

J.P. Grossman, J.K. Salmon, C.R. Ho, D.J. Ierardi, B. Towles, B. Batson, J. Spengler, S.C. Wang, R. Mueller, M. Theobald, C. Young, J. Gagliardo, M.M. Deneroff, R.O. Dror, and D.E. Shaw. Hierarchical Simulation-Based Verification of Anton, a Special-Purpose Parallel Machine. Proceedings of the 26th IEEE International Conference on Computer Design (ICCD '08), Lake Tahoe, California (2008)

J.P. Grossman, C. Young, J.A. Bank, K. Mackenzie, D.J. Ierardi, J.K. Salmon, R.O. Dror, and D.E. Shaw. Simulation and Embedded Software Development for Anton, a Parallel Machine with Heterogeneous Multicore ASICs. Proceedings of the 6th IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES/ISSS '08), Atlanta, Georgia (2008)

D.E. Shaw, M.M. Deneroff, R.O. Dror, J.S. Kuskin, R.H. Larson, J.K. Salmon, C. Young, B. Batson, K.J. Bowers, J.C. Chao, M.P. Eastwood, J. Gagliardo, J.P. Grossman, C.R. Ho, D.J. Ierardi, I. Kolossvary, J.L. Klepeis, T. Layman, C. McLeavey, M.A. Moraes, R. Mueller, E.C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, and S.C. Wang. Anton, A Special-Purpose Machine for Molecular Dynamics Simulation. Communications of the ACM 51:91-97 (2008)

C.R. Ho, M. Theobald, M.M. Deneroff, R.O. Dror, J. Gagliardo, and D.E. Shaw, Early Formal Verification of Conditional Coverage Points to Identify Intrinsically Hard-to-Verify Logic. Proceedings of the 45th Annual Design Automation Conference (DAC '08) , Anaheim, California (2008)

P. Maragakis, K. Lindorff-Larsen, M.P. Eastwood, R.O. Dror, J.L. Klepeis, I.T. Arkin, M.Ø. Jensen, H. Xu, N. Trbovic, R.A. Friesner, A.G. Palmer, and D.E. Shaw. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. Journal of Physical Chemistry B 112:6155-6158 (2008)

R.H. Larson, J.K. Salmon, R.O. Dror, M.M. Deneroff, R.C. Young, J.P. Grossman, Y. Shan, J.L. Klepeis, and D.E. Shaw. High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. Proceedings of the 14th International Symposium on High-Performance Computer Architecture, Salt Lake City, Utah (2008)

J.S. Kuskin, R.C. Young, J.P. Grossman, B. Batson, M.M. Deneroff, R.O. Dror, and D.E. Shaw. Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation. Proceedings of the 14th International Symposium on High-Performance Computer Architecture, Salt Lake City, Utah (2008)