Resources

Software

  • Desmond: An MD simulation software package that runs on certain commodity GPUs. We make Desmond available at no cost for use by faculty members, researchers, and/or students at academic and not‑for‑profit institutions.

Simulation Time on Anton

Publications

  • 2024
  • Huafeng Xu, Timothy Palpant, Qi Wang, and David E. Shaw, “Design of antigens to present a tumor‑specific cryptic epitope,” bioRxiv preprint, bioRxiv 2024.04.15.588917, 2024. Text
  • Andreas Varkaris, Ermira Pazolli, Hakan Gunaydin, Qi Wang, Levi Pierce, Alessandro A. Boezio, Artemisa Bulku, Lucian DiPietro, Cary Fridrich, Adam Frost, Fabrizio Giordanetto, Erika P. Hamilton, Katherine Harris, Michael Holliday, Tamieka L. Hunter, Amanda Iskandar, Yongli Ji, Alexandre Larivée, Jonathan R. LaRochelle, André Lescarbeau, Fabien Llambi, Brenda Lormil, Mary M. Mader, Brenton G. Mar, Iain Martin, Thomas H. McLean, Klaus Michelsen, Yakov Pechersky, Erika Puente‑Poushnejad, Kevin Raynor, Dipali Rogala, Ramin Samadani, Alison M. Schram, Kelley Shortsleeves, Sweta Swaminathan, Shahein Tajmir, Gege Tan, Yong Tang, Roberto Valverde, Bryan Wehrenberg, Jeremy Wilbur, Bret R. Williams, Hongtao Zeng, Hanmo Zhang, W. Patrick Walters, Beni B. Wolf, David E. Shaw, Donald A. Bergstrom, James Watters, James S. Fraser, Pascal D. Fortin, and D. Randal Kipp, “Discovery and Clinical Proof‑of‑Concept of RLY‑2608, a First‑in‑Class Mutant‑Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia,” Cancer Discovery, vol. 14, no. 2, 2024, pp. 240–257. Text
  • Heike Schönherr, Pelin Ayaz, Alexander M. Taylor, Jessica B. Casaletto, B. Barry Touré, Demetri T. Moustakas, Brandi M. Hudson, Roberto Valverde, Songping Zhao, Patrick J. O’Hearn, Lindsey Foster, Dina A. Sharon, Sam Garfinkle, Fabrizio Giordanetto, André Lescarbeau, Ravi Kurukulasuriya, Nastaran Gerami‑Moayed, Dejan Maglic, Kamil Bruderek, Gaauri Naik, Hakan Gunaydin, Mary M. Mader, Alessandro A. Boezio, Thomas H. McLean, Rongfeng Chen, Yanxia Wang, David E. Shaw, James Watters, and Donald A. Bergstrom, “Discovery of Lirafugratinib (RLY‑4008), a Highly Selective Irreversible Small‑Molecule Inhibitor of FGFR2,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 6, 2024, e2317756121. Text
  • Cristian Predescu, Michael Snarski, Avi Robinson‑Mosher, Duluxan Sritharan, Tamas Szalay, and David E. Shaw, “Times Square Sampling: An Adaptive Algorithm for Free Energy Estimation,” Journal of Computational and Graphical Statistics, vol. 33, no. 3, 2024, pp. 1073–1083. Text
  • 2023
  • Heidi Koldsø, Morten Ø. Jensen, Vishwanath Jogini, and David E. Shaw, “Functional Dynamics and Allosteric Modulation of TRPA1,” Structure, vol. 31, no. 12, 2023, pp. 1556–1566. Text
  • Vivek Subbiah, Vaibhav Sahai, Dejan Maglic, Kamil Bruderek, B. Barry Touré, Songping Zhao, Roberto Valverde, Patrick J. O’Hearn, Demetri T. Moustakas, Heike Schönherr, Nastaran Gerami‑Moayed, Alexander M. Taylor, Brandi M. Hudson, Damian J. Houde, Debjani Pal, Lindsey Foster, Hakan Gunaydin, Pelin Ayaz, Dina A. Sharon, Lipika Goyal, Alison M. Schram, Suneel Kamath, Cori Ann Sherwin, Oleg Schmidt‑Kittler, Kai Yu Jen, Fabien Ricard, Beni B. Wolf, David E. Shaw, Donald A. Bergstrom, James Watters, and Jessica B. Casaletto, “RLY‑4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations,” Cancer Discovery, vol. 13, no. 9, 2023, pp. 2012–2031. Text
  • Christine Y. Yeh, Jesus A. Izaguirre, Jack B. Greisman, Lindsay Willmore, Paul Maragakis, and David E. Shaw, “A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis,” Journal of Chemical Information and Modeling, vol. 63, no. 13, 2023, pp. 4115–4124. Text
  • Jussi Aittoniemi, Morten Ø. Jensen, Albert C. Pan, and David E. Shaw, “Desensitization Dynamics of the AMPA Receptor,” Structure, vol. 31, no. 6, 2023, pp. 724–734. Text
  • Jack B. Greisman, Lindsay Willmore, Christine Y. Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, and David E. Shaw, “Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X‑ray Crystallography,” Journal of Chemical Information and Modeling, vol. 63, no. 9, 2023, pp. 2644–2650. Text
  • Pelin Ayaz, Agatha Lyczek, YiTing Paung, Victoria R. Mingione, Roxana E. Iacob, Parker W. de Waal, John R. Engen, Markus A. Seeliger, Yibing Shan, and David E. Shaw, “Structural Mechanism of a Drug‑Binding Process Involving a Large Conformational Change of the Protein Target,” Nature Communications, vol. 14, 2023, 1885. Text
  • Vishwanath Jogini, Morten Ø. Jensen, and David E. Shaw, “Gating and Modulation of an Inward‑Rectifier Potassium Channel,” Journal of General Physiology, vol. 155, no. 2, 2023, e202213085. Text
  • 2022
  • Huafeng Xu, Timothy Palpant, Cody Weinberger, and David E. Shaw, “Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin,” Journal of Chemical Theory and Computation, vol. 18, no. 8, 2022, pp. 4995–5005. Text
  • Maxwell R. Tucker, Stefano Piana, Dazhi Tan, Michael V. LeVine, and David E. Shaw, “Development of Force Field Parameters for the Simulation of Single‑ and Double‑Stranded DNA Molecules and DNA‑Protein Complexes,” The Journal of Physical Chemistry B, vol. 126, no. 24, 2022, pp. 4442–4457. Text
  • Keun Sup Shim, Brian Greskamp, Brian Towles, Bruce Edwards, J.P. Grossman, David E. Shaw, “The Specialized High‑Performance Network on Anton 3,” Proceedings of the 28th Annual International Symposium on High‑Performance Computer Architecture (HPCA ’22), New York, NY: IEEE, 2022, pp. 1211–1223. Text
  • James Chen, Qi Wang, Brandon Malone, Eliza Llewellyn, Yakov Pechersky, Kashyap Maruthi, Ed T. Eng, Jason K. Perry, Elizabeth A. Campbell, David E. Shaw, and Seth A. Darst, “Ensemble Cryo‑Electron Microscopy Reveals Conformational States of the nsp13 Helicase in the SARS‑CoV‑2 Helicase Replication‑Transcription Complex,” Nature Structural & Molecular Biology, vol. 29, 2022, pp. 250–260. Text
  • Marcia R. Campbell, Ana Ruiz‑Saenz, Elliott Peterson, Christopher Agnew, Pelin Ayaz, Sam Garfinkle, Peter Littlefield, Veronica Steri, Julie Oeffinger, Maryjo Sampang, Yibing Shan, David E. Shaw, Natalia Jura, and Mark M. Moasser, “Targetable HER3 Functions Driving Tumorigenic Signaling in HER2‑Amplified Cancers,” Cell Reports, vol. 38, no. 5, 2022, 110291. Text
  • Yibing Shan, Venkatesh P. Mysore, Abba E. Leffler, Eric T. Kim, Shiori Sagawa, and David E. Shaw, “How Does a Small Molecule Bind at a Cryptic Binding Site?,” PLOS Computational Biology, vol. 18, no. 3, 2022, e1009817. Text
  • Paul Robustelli, Alain Ibanez‑de‑Opakua, Cecily Campbell‑Bezat, Fabrizio Giordanetto, Stefan Becker, Markus Zweckstetter, Albert C. Pan, and David E. Shaw, “Molecular Basis of Small‑Molecule Binding to α‑synuclein,” Journal of the American Chemical Society, vol. 144, no. 6, 2022, pp. 2501–2510. Text
  • 2021
  • Brandon Malone, James Chen, Qi Wang, Eliza Llewellyn, Young Joo Choi, Paul Dominic B. Olinares, Xinyun Cao, Carolina Hernandez, Edward T. Eng, Brian T. Chait, David E. Shaw, Robert Landick, Seth A. Darst, and Elizabeth A. Campbell, “Structural Basis for Backtracking by the SARS‑CoV‑2 Replication‑Transcription Complex,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 19, 2021, e2102516118. Text
  • Venkatesh P. Mysore, Zhi‑Wei Zhou, Chiara Ambrogio, Lianbo Li, Jonas N. Kapp, Chunya Lu, Qi Wang, Maxwell R. Tucker, Jeffrey J. Okoro, Gabriela Nagy‑Davidescu, Xiaochen Bai, Andreas Plückthun, Pasi A. Jänne, Kenneth D. Westover, Yibing Shan, and David E. Shaw, “A Structural Model of a Ras–Raf Signalosome,” Nature Structural & Molecular Biology, vol. 28, no. 10, 2021, pp. 847–857. Text
  • 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, and Kevin A. Yuh, “Anton 3: Twenty Microseconds of Molecular Dynamics Simulation Before Lunch,” Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC21), New York, NY: ACM, 2021. Text
  • Anna‑Lena Unterweger, Morten Ø. Jensen, Fabrizio Giordanetto, Vishwanath Jogini, Alena Rüscher, Marietta Seuß, Paula Winkelmann, Leandra Koletzko, David E. Shaw, Matthias Siebeck, Roswitha Gropp, Florian Beigel, and Attila Aszodi, “Suppressing Kv1.3 Ion Channel Activity with a Novel Small Molecule Inhibitor Ameliorates Inflammation in a Humanised Mouse Model of Ulcerative Colitis,” Journal of Crohn’s & Colitis, vol. 15, no. 11, 2021, 1943–1958. Text
  • Christopher Agnew, Pelin Ayaz, Risa Kashima, Hanna S. Loving, Prajakta Ghatpande, Jennifer E. Kung, Eric S. Underbakke, Yibing Shan, David E. Shaw, Akiko Hata, and Natalia Jura, “Structural Basis for ALK2/BMPR2 Receptor Complex Signaling through Kinase Domain Oligomerization,” Nature Communications, vol. 12, 2021, 4950. Text
  • Alexander G. Donchev, Andrew G. Taube, Elizabeth Decolvenaere, Cory Hargus, Robert T. McGibbon, Ka‑Hei Law, Brent A. Gregersen, Je‑Luen Li, Kim Palmo, Karthik Siva, Michael Bergdorf, John L. Klepeis, and David E. Shaw, “Quantum Chemical Benchmark Databases of Gold‑Standard Dimer Interaction Energies,” Scientific Data, vol. 8, 2021, 55. Text
  • Christos Adamopoulos, Tamer A. Ahmed, Maxwell R. Tucker, Peter M.U. Ung, Min Xiao, Zoi Karoulia, Angelo Amabile, Xuewei Wu, Stuart A. Aaronson, Celina Ang, Vito W. Rebecca, Brian D. Brown, Avner Schlessinger, Meenhard Herlyn, Qi Wang, David E. Shaw, and Poulikos I. Poulikakos, “Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy‑Resistant Tumors Driven by Oncogenic BRAF Signaling,” Cancer Discovery, vol. 11, no. 7, 2021, pp. 1716–1735. Text
  • 2020
  • Cristian Predescu, Michael Bergdorf, and David E. Shaw, “Midtown Splines: An Optimal Charge Assignment for Electrostatics Calculations,” The Journal of Chemical Physics, vol. 153, no. 22, 2020, 224117. Text
  • Paul Maragakis, Hunter Nisonoff, Brian Cole, and David E. Shaw, “A Deep‑Learning View of Chemical Space Designed to Facilitate Drug Discovery,” Journal of Chemical Information and Modeling, vol. 60, no. 10, 2020, pp. 4487–4496. Text
  • John J. Cherian, Andrew G. Taube, Robert T. McGibbon, Panagiotis Angelikopoulos, Guy Blanc, Michael Snarski, Daniel D. Richman, John L. Klepeis, and David E. Shaw, “Efficient Hyperparameter Optimization by Way of PAC‑Bayes Bound Minimization,” arXiv preprint, arXiv:2008.06431, 2020. Text
  • Siduo Jiang, Miklos Feher, Chris Williams, Brian Cole, and David E. Shaw, “AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets,” Journal of Chemical Information and Modeling, vol. 60, no. 9, 2020, pp. 4326–4338. Text
  • Paul Robustelli, Stefano Piana, and David E. Shaw, “Mechanism of Coupled Folding‑upon‑Binding of an Intrinsically Disordered Protein” Journal of the American Chemical Society, vol. 142, no. 25, 2020, pp. 11092–11101. Text
  • Xiao‑E Yan, Pelin Ayaz, Su‑Jie Zhu, Peng Zhao, Ling Liang, Casey H. Zhang, Ya‑Chuang Wu, Je‑Luen Li, Hwan Geun Choi, Xin Huang, Yibing Shan, David E. Shaw, and Cai‑Hong Yun, “Structural Basis of AZD9291 Selectivity for EGFR T790M,” Journal of Medicinal Chemistry, vol. 63, no. 15, 2020, pp. 8502–8511. Text
  • Cristian Predescu, Adam K. Lerer, Ross A. Lippert, Brian Towles, J.P. Grossman, Robert M. Dirks, and David E. Shaw, “The u‑series: A Separable Decomposition for Electrostatics Computation with Improved Accuracy,” The Journal of Chemical Physics, vol. 152, no. 8, 2020, 084113. Text
  • Stefano Piana, Paul Robustelli, Dazhi Tan, Songela Chen, and David E. Shaw, “Development of a Force Field for the Simulation of Single‑Chain Proteins and Protein–Protein Complexes” Journal of Chemical Theory and Computation, vol. 16, no. 4, 2020, pp. 2494–2507. Text
  • 2019
  • Pelin Ayaz, Henrik M. Hammarén, Juuli Raivola, Dina Sharon, Stevan R. Hubbard, Olli Silvennoinen, Yibing Shan, and David E. Shaw, “Structural Models of Full‑Length JAK2 Kinase,” bioRxiv preprint, bioRxiv:727727, 2019. Text
  • Qi Wang, Yakov Pechersky, Shiori Sagawa, Albert C. Pan, and David E. Shaw, “Structural Mechanism for Bruton’s Tyrosine Kinase Activation at the Cell Membrane,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 19, 2019, pp. 9390–9399. Text
  • Fabrizio Giordanetto, Chentian Jin, Lindsay Willmore, Miklos Feher, and David E. Shaw, “Fragment Hits: What Do They Look Like and How Do They Bind?” Journal of Medicinal Chemistry, vol. 62, no. 7, 2019, pp. 3381–3394. Text
  • Albert C. Pan, Daniel Jacobson, Konstantin Yatsenko, Duluxan Sritharan, Thomas M. Weinreich, and David E. Shaw, “Atomic‑Level Characterization of Protein–Protein Association,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 10, 2019, pp. 4244–4249. Text
  • 2018
  • Laura C. Zanetti‑Domingues, Dimitrios Korovesis, Sarah R. Needham, Christopher J. Tynan, Shiori Sagawa, Selene K. Roberts, Antonija Kuzmanic, Elena Ortiz‑Zapater, Purvi Jain, Rob C. Roovers, Alireza Lajevardipour, Paul M. P. van Bergen en Henegouwen, George Santis, Andrew H. A. Clayton, David T. Clarke, Francesco L. Gervasio, Yibing Shan, David E. Shaw, Daniel J. Rolfe, Peter J. Parker, and Marisa L. Martin‑Fernandez, “The Architecture of EGFR’s Basal Complexes Reveals Autoinhibition Mechanisms in Dimers and Oligomers,” Nature Communications, vol. 9, 2018, 4325. Text
  • Stefano Piana and David E. Shaw, “Atomic‑Level Description of Protein Folding inside the GroEL Cavity,” The Journal of Physical Chemistry B, vol. 122, no. 49, 2018, pp. 11440–11449. Text
  • Matthieu Masureel, Yaozhong Zou, Louis‑Philippe Picard, Emma van der Westhuizen, Jacob P. Mahoney, João P. G. L. M. Rodrigues, Thomas J. Mildorf, Ron O. Dror, David E. Shaw, Michel Bouvier, Els Pardon, Jan Steyaert, Roger K. Sunahara, William I. Weis, Cheng Zhang, and Brian K. Kobilka, “Structural Insights into Binding Specificity, Efficacy and Bias of a β2AR Partial Agonist,” Nature Chemical Biology, vol. 14, no. 11, 2018, pp. 1059–1066. Text
  • Michael P. Bokoch, Hyunil Jo, James R. Valcourt, Yoga Srinivasan, Albert C. Pan, Sara Capponi, Michael Grabe, Ron O. Dror, David E. Shaw, William F. DeGrado, and Shaun R. Coughlin, “Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein‑Coupled Receptor by a Lipophilic Small Molecule,” Biochemistry, vol. 57, no. 39, 2018, pp. 5748–5758. Text
  • Paul Robustelli, Stefano Piana, and David E. Shaw, “Developing a Molecular Dynamics Force Field for Both Folded and Disordered Protein States,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 21, 2018, pp. E4758–E4766. Text
  • Xianqiang Song, Morten Ø. Jensen, Vishwanath Jogini, Richard A. Stein, Chia‑Hsueh Lee, Hassane S. Mchaourab, David E. Shaw, and Eric Gouaux, “Mechanism of NMDA Receptor Channel Block by MK‑801 and Memantine,” Nature, vol. 556, no. 7702, 2018, pp. 515–519. Text
  • Dazhi Tan, Stefano Piana, Robert M. Dirks, and David E. Shaw, “RNA Force Field with Accuracy Comparable to State‑of‑the‑Art Protein Force Fields,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 7, 2018, pp. E1346–E1355. Text
  • 2017
  • Robert T. McGibbon, Andrew G. Taube, Alexander G. Donchev, Karthik Siva, Felipe Hernández, Cory Hargus, Ka‑Hei Law, John L. Klepeis, and David E. Shaw, “Improving the Accuracy of Møller‑Plesset Perturbation Theory with Neural Networks,” Journal of Chemical Physics, vol. 147, no. 16, 2017, 161725. Text
  • Albert C. Pan, Huafeng Xu, Timothy Palpant, and David E. Shaw, “Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations,” Journal of Chemical Theory and Computation, vol. 13, no. 7, 2017, pp. 3372–3377. Text
  • Smriti Sangwan, Anni Zhao, Katrina L. Adams, Christina K. Jayson, Michael R. Sawaya, Elizabeth L. Guenther, Albert C. Pan, Jennifer Ngo, Destaye M. Moore, Angela B. Soriaga, Thanh D. Do, Lukasz Goldschmidt, Rebecca Nelson, Michael T. Bowers, Carla M. Koehler, David E. Shaw, Bennett G. Novitch, and David S. Eisenberg, “Atomic Structure of a Toxic, Oligomeric Segment of SOD1 Linked to Amyotrophic Lateral Sclerosis (ALS),” Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 33, 2017, pp. 8770–8775. Text
  • 2016
  • Albert C. Pan, Thomas M. Weinreich, Stefano Piana, and David E. Shaw, “Demonstrating an Order‑of‑Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems,” Journal of Chemical Theory and Computation, vol. 12, no. 3, 2016, pp. 1360–1367. Text
  • Huafeng Xu and David E. Shaw, “A Simple Model of Multivalent Adhesion and Its Application to Influenza Infection,” Biophysical Journal, vol. 110, no. 1, 2016, pp. 218–233. Text
  • Sarah R. Needham, Selene K. Roberts, Anton Arkhipov, Venkatesh P. Mysore, Christopher J. Tynan, Laura C. Zanetti‑Domingues, Eric T. Kim, Valeria Losasso, Dimitrios Korovesis, Michael Hirsch, Daniel J. Rolfe, David T. Clarke, Martyn D. Winn, Alireza Lajevardipour, Andrew H. A. Clayton, Linda J. Pike, Michela Perani, Peter J. Parker, Yibing Shan, David E. Shaw, and Marisa L. Martin‑Fernandez, “EGFR Oligomerization Organizes Kinase‑Active Dimers into Competent Signalling Platforms,” Nature Communications, vol. 7, 2016, 13307. Text
  • Kresten Lindorff‑Larsen, Paul Maragakis, Stefano Piana, and David E. Shaw, “Picosecond to Millisecond Structural Dynamics in Human Ubiquitin,” The Journal of Physical Chemistry B, vol. 120, no. 33, 2016, pp. 8313–8320. Text
  • Alpan Raval, Stefano Piana, Michael P. Eastwood, and David E. Shaw, “Assessment of the Utility of Contact‑Based Restraints in Accelerating the Prediction of Protein Structure Using Molecular Dynamics Simulations,” Protein Science, vol. 25, no. 1, 2016, pp. 19–29. Text
  • Dong Guo, Albert C. Pan, Ron O. Dror, Tamara Mocking, Rongfang Liu, Laura H. Heitman, David E. Shaw, and Adriaan P. IJzerman, “Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor,” Molecular Pharmacology, vol. 89, no. 5, 2016, pp. 485–491. Text
  • 2015
  • J.P. Grossman, Brian Towles, Brian Greskamp, and David E. Shaw, “Filtering, Reductions and Synchronization in the Anton 2 Network,” Proceedings of the 29th IEEE International Parallel and Distributed Processing Symposium (IPDPS ’15), Hyderabad, India: IEEE Computer Society, 2015, pp. 860–870. Text
    Best Paper Award, Architecture Track.
  • Ron O. Dror, Thomas J. Mildorf, Daniel Hilger, Aashish Manglik, David W. Borhani, Daniel H. Arlow, Ansgar Philippsen, Nicolas Villanueva, Zhongyu Yang, Michael T. Lerch, Wayne L. Hubbell, Brian K. Kobilka, Roger K. Sunahara, David E. Shaw, “Structural Basis for Nucleotide Exchange in Heterotrimeric G Proteins,” Science, vol. 348, no. 6241, 2015, pp. 1361–1365. Text
  • Hoi Sung Chung, Stefano Piana, David E. Shaw, and William A. Eaton, “Structural Origin of Slow Diffusion in Protein Folding,” Science, vol. 349, no. 6255, 2015, pp. 1504–1510. Text
  • Huafeng Xu, Aaron G. Schmidt, Timothy O’Donnell, Matthew D. Therkelsen, Thomas B. Kepler, M. Anthony Moody, Barton F. Haynes, Hua‑Xin Liao, Stephen C. Harrison, and David E. Shaw, “Key Mutations Stabilize Antigen‑Binding Conformation during Affinity Maturation of a Broadly Neutralizing Influenza Antibody Lineage,” Proteins: Structure, Function, and Bioinformatics, vol. 83, no. 4, 2015, pp. 771–780. Text
  • Zachariah H. Foda, Yibing Shan, Eric T. Kim, David E. Shaw, and Markus A. Seeliger, “A Dynamically Coupled Allosteric Network Underlies Binding Cooperativity in Src Kinase,” Nature Communications, vol. 6, 2015, 5939. Text
  • Stefano Piana, Alexander G. Donchev, Paul Robustelli, and David E. Shaw, “Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States,” The Journal of Physical Chemistry B, vol. 119, no. 16, 2015, pp. 5113–5123. Text
  • Zhou Fan, Ron O. Dror, Thomas J. Mildorf, Stefano Piana, and David 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, vol. 112, no. 24, 2015, pp. 7454–7459. Text
  • Jessica R. Ingram, Kevin E. Knockenhauer, Benedikt M. Markus, Joseph Mandelbaum, Alexander Ramek, Yibing Shan, David E. Shaw, Thomas U. Schwartz, Hidde L. Ploegh, and Sebastian Lourido, “Allosteric Activation of Apicomplexan Calcium‑Dependent Protein Kinases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 36, 2015, pp. E4975–E4984. Text
  • Lorenzo Sborgi, Abhinav Verma, Stefano Piana, Kresten Lindorff‑Larsen, Michele Cerminara, Clara M. Santiveri, David E. Shaw, Eva de Alba, and Victor Muñoz, “Interaction Networks in Protein Folding via Atomic‑Resolution Experiments and Long‑Timescale Molecular Dynamics Simulations,” Journal of the American Chemical Society, vol. 137, no. 20, 2015, pp. 6506–6516. Text
  • 2014
  • Ryan Ferro, Hao Zhou, Yibing Shan, Qun Liu, David E. Shaw, Xiaoxia Li, and Hao Wu, “IRAK4 Dimerization and Trans‑Autophosphorylation Are Induced by Myddosome Assembly,” Molecular Cell, vol. 55, no. 6, 2014, pp. 891–903. Text
  • Peter Littlefield, Lijun Liu, Venkatesh Mysore, Yibing Shan, David E. Shaw, and Natalia Jura, “Structural Analysis of the EGFR/HER3 Heterodimer Reveals the Molecular Basis for Activating HER3 Mutations,” Science Signaling, vol. 7, no. 354, 2014, ra114. Text
  • 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 S. 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 P. 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, and Cliff 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, 2014, pp. 41–53. Text
    Gordon Bell Prize.
  • Yibing Shan, Kavitha Gnanasambandan, Daniela Ungureanu, Eric T. Kim, Henrik Hammarén, Kazuo Yamashita, Olli Silvennoinen, David E. Shaw, and Stevan R. Hubbard, “Molecular Basis for Pseudokinase‑Dependent Autoinhibition of JAK2 Tyrosine Kinase,” Nature Structural & Molecular Biology, vol. 21, no. 7, 2014, pp. 579–584. Text
  • Albert C. Pan, Thomas M. Weinreich, Yibing Shan, Daniele P. Scarpazza, and David E. Shaw, “Assessing the Accuracy of Two Enhanced Sampling Methods Using EGFR Kinase Transition Pathways: The Influence of Collective Variable Choice,” Journal of Chemical Theory and Computation, vol. 10, no. 7, 2014, pp. 2860–2865. Text
  • Brian Towles, J.P. Grossman, Brian Greskamp, and David E. Shaw, “Unifying On‑Chip and Inter‑Node Switching Within the Anton 2 Network,” Proceedings of the 41st International Symposium on Computer Architecture (ISCA ’14), Minneapolis, MN: IEEE, 2014, pp. 1–12.Text
  • Anton Arkhipov, Yibing Shan, Eric T. Kim, and David E. Shaw, “Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor,” PLOS Computational Biology, vol. 10, no. 7, 2014, e1003742. Text
  • Stefano Piana, John L. Klepeis, and David E. Shaw, “Assessing the Accuracy of Physical Models Used in Protein‑Folding Simulations: Quantitative Evidence from Long Molecular Dynamics Simulations,” Current Opinion in Structural Biology, vol. 24, 2014, pp. 98–105. Text
  • Jennifer M. Kavran, Jacqueline M. McCabe, Patrick O. Byrne, Mary Katherine Connacher, Zhihong Wang, Alexander Ramek, Sarvenaz Sarabipour, Yibing Shan, David E. Shaw, Kalina Hristova, Philip A. Cole, and Daniel J. Leahy, “How IGF‑1 Activates its Receptor,” eLife, vol. 3, 2014, e03772. Text
  • 2013
  • Daniele P. 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, and David 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 ’13), Boston, MA: IEEE Computer Society, 2013, pp. 933–945. Text
    Best Paper Award, Applications Track.
  • Ron O. Dror, Hillary F. Green, Celine Valant, David W. Borhani, James R. Valcourt, Albert C. Pan, Daniel H. Arlow, Meritxell Canals, J. Robert Lane, Raphaël Rahmani, Jonathan B. Baell, Patrick M. Sexton, Arthur Christopoulos, and David E. Shaw, “Structural Basis for Modulation of a G‑Protein‑Coupled Receptor by Allosteric Drugs,” Nature, vol. 503, no. 7475, 2013, pp. 295–299. Text
  • Ross A. Lippert, Cristian Predescu, Douglas J. Ierardi, Kenneth M. Mackenzie, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, “Accurate and Efficient Integration for Molecular Dynamics Simulations at Constant Temperature and Pressure,” Journal of Chemical Physics, vol. 139, no. 16, 2013, 164106. Text
  • Anton Arkhipov, Yibing Shan, Rahul Das, Nicholas F. Endres, Michael P. Eastwood, David E. Wemmer, John Kuriyan, and David E. Shaw, “Architecture and Membrane Interactions of the EGF Receptor,” Cell, vol. 152, no. 3, 2013, pp. 557–569. Text
  • Nicholas F. Endres, Rahul Das, Adam W. Smith, Anton Arkhipov, Erika Kovacs, Yongjian Huang, Jeffrey G. Pelton, Yibing Shan, David E. Shaw, David E. Wemmer, Jay T. Groves, and John Kuriyan, “Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor,” Cell, vol. 152, no. 3, 2013, pp. 543–556. Text
  • J.P. Grossman, Brian Towles, Joseph A. Bank, and David E. Shaw, “The Role of Cascade, a Cycle‑Based Simulation Infrastructure, in Designing the Anton Special‑Purpose Supercomputers,” Proceedings of the 50th Annual Design Automation Conference (DAC ’13), Austin, TX, June 2–6, 2013. Text
  • J.P. Grossman, Jeffrey S. Kuskin, Joseph A. Bank, Michael Theobald, Ron O. Dror, Douglas J. Ierardi, Richard H. Larson, U. Ben Schafer, Brian Towles, Cliff Young, and David 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 ’13), New York: NY: ACM, 2013, pp. 549–560. Text
  • Stefano Piana, Kresten Lindorff‑Larsen, and David E. Shaw, “Atomistic Description of the Folding of a Dimeric Protein,” The Journal of Physical Chemistry B, vol. 117, no. 42, 2013, pp. 12935–12942. Text
  • Anton Arkhipov, Yibing Shan, Eric T. Kim, Ron O. Dror, and David E. Shaw, “Her2 Activation Mechanism Reflects Evolutionary Preservation of Asymmetric Ectodomain Dimers in the Human EGFR Family,” eLife, vol. 2, 2013, e00708. Text
  • Yibing Shan, Anton Arkhipov, Eric T. Kim, Albert C. Pan, and David E. Shaw, “Transitions to Catalytically Inactive Conformations in EGFR Kinase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 18, 2013, pp. 7270–7275. Text
  • Rie Nygaard, Yaozhong Zou, Ron O. Dror, Thomas J. Mildorf, Daniel H. Arlow, Aashish Manglik, Albert C. Pan, Corey W. Liu, Juan Jose Fung, Michael P. Bokoch, Foon Sun Thian, Tong Sun Kobilka, David E. Shaw, Luciano Mueller, R. Scott Prosser, and Brian K. Kobilka, “The Dynamic Process of β2‑Adrenergic Receptor Activation,” Cell, vol. 152, no. 3, 2013, pp. 532–542. Text
  • Morten Ø. Jensen, Vishwanath Jogini, Michael P. Eastwood, and David E. Shaw, “Atomic‑Level Simulation of Current–Voltage Relationships in Single‑File Ion Channels,” The Journal of General Physiology, vol. 141, no. 5, 2013, pp. 619–632. Text
  • Aaron G. Schmidt, Huafeng Xu, Amir R. Khana, Timothy O’Donnell, Surender Khurana, Lisa R. King, Jody Manischewitz, Hana Golding, Pirada Suphaphiphat, Andrea Carfi, Ethan C. Settembre, Philip R. Dormitzer, Thomas B. Kepler, Ruijun Zhang, M. Anthony Moody, Barton F. Haynes, Hua‑Xin Liao, David E. Shaw, and Stephen C. Harrison, “Preconfiguration of the Antigen‑Binding Site During Affinity Maturation of a Broadly Neutralizing Influenza Virus Antibody,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 1, 2013, pp. 264–269. Text
  • Albert C. Pan, David W. Borhani, Ron O. Dror, and David E.  Shaw, “Molecular Determinants of Drug–Receptor Binding Kinetics,” Drug Discovery Today, vol. 18, no. 13–14, 2013, pp. 667–673. Text
  • Stefano Piana, Kresten Lindorff‑Larsen, and David E. Shaw, “Atomic‑Level Description of Ubiquitin Folding,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 15, 2013, pp. 5915–5920. Text
  • Michael P. Eastwood, Tarun Chitra, John M. Jumper, Kim Palmo, Albert C. Pan, and David E. Shaw, “Rotational Relaxation in ortho‑Terphenyl: Using Atomistic Simulations to Bridge Theory and Experiment,” The Journal of Physical Chemistry B, vol. 117, no. 42, 2013, pp. 12898–12907. Text
  • Tae Hun Kim, Ka Young Chung, Aashish Manglik, Alexandar L. Hansen, Ron O. Dror, Thomas J. Mildorf, David E. Shaw, Brian K. Kobilka, and R. Scott Prosser, “The Role of Ligands on the Equilibria Between Functional States of a G Protein‑Coupled Receptor,” Journal of the American Chemical Society, vol. 135, no. 25, 2013, pp. 9465–9474. Text
  • 2012
  • Morten Ø. Jensen, Vishwanath Jogini, David W. Borhani, Abba E. Leffler, Ron O. Dror, and David E. Shaw, “Mechanism of Voltage Gating in Potassium Channels,” Science, vol. 336, no. 6078, 2012, pp. 229–233. Text
  • Yibing Shan, Michael P. Eastwood, Xuewu Zhang, Eric T. Kim, Anton Arkhipov, Ron O. Dror, John Jumper, John Kuriyan, and David E. Shaw, “Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization,” Cell, vol. 149, no. 4, 2012, pp. 860–870. Text
  • Stefano Piana, Kresten Lindorff‑Larsen, and David E. Shaw, “Protein Folding Kinetics and Thermodynamics from Atomistic Simulation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 44, 2012, pp. 17845–17850. Text
  • Cheng Zhang, Yoga Srinivasan, Daniel H. Arlow, Juan Jose Fung, Daniel Palmer, Yaowu Zheng, Hillary F. Green, Anjali Pandey, Ron O. Dror, David E. Shaw, William I. Weis, Shaun R. Coughlin, and Brian K. Kobilka, “High‑Resolution Crystal Structure of Human Protease‑Activated Receptor 1,” Nature, vol. 492, no. 7429, 2012, pp. 387–392. Text
  • Stefano Piana, Kresten Lindorff‑Larsen, Robert M. Dirks, John K. Salmon, Ron O. Dror, and David E. Shaw, “Evaluating the Effects of Cutoffs and Treatment of Long‑range Electrostatics in Protein Folding Simulations,” PLOS ONE, vol. 7, no. 6, 2012, e39918. Text
  • Cristian Predescu, Ross A. Lippert, Michael P. Eastwood, Douglas Ierardi, Huafeng Xu, Morten Ø. Jensen, Kevin J. Bowers, Justin Gullingsrud, Charles A. Rendleman, Ron O. Dror, and David E. Shaw, “Computationally Efficient Molecular Dynamics Integrators with Improved Sampling Accuracy,” Molecular Physics, vol. 110, no. 9–10, 2012, pp. 967–983. Text
  • Kresten Lindorff‑Larsen, Nikola Trbovic, Paul Maragakis, Stefano Piana, and David E. Shaw, “Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation,” Journal of the American Chemical Society, vol. 336, no. 8, 2012, pp. 3787–3791. Text
  • Alpan Raval, Stefano Piana, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, “Refinement of Protein Structure Homology Models via Long, All‑Atom Molecular Dynamics Simulations,” Proteins: Structure, Function, and Bioinformatics, vol. 80, no. 8, 2012, pp. 2071–2079. Text
  • Kresten Lindorff‑Larsen, Paul Maragakis, Stefano Piana, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, “Systematic Validation of Protein Force Fields against Experimental Data,” PLOS ONE, vol. 7, no. 2, 2012, e32131. Text
  • Robert M. Dirks, Huafeng Xu, and David E. Shaw, “Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations,” Journal of Chemical Theory and Computation, vol. 8, no. 1, 2012, pp. 162–171. Text
  • Ron O. Dror, Robert M. Dirks, J.P. Grossman, Huafeng Xu, and David E. Shaw, “Biomolecular Simulation: A Computational Microscope for Molecular Biology,” Annual Review of Biophysics, vol. 41, 2012, pp. 429–452. Text
  • Andrew C. Kruse, Jianxin Hu, Albert C. Pan, Daniel H. Arlow, Daniel M. Rosenbaum, Erica Rosemond, Hillary F. Green, Tong Liu, Pil Seok Chae, Ron O. Dror, David E. Shaw, William I. Weis, Jürgen Wess, and Brian K. Kobilka, “Structure and Dynamics of the M3 Muscarinic Acetylcholine Receptor,” Nature, vol. 482, no. 7386, 2012, pp. 552–556. Text
  • Moon Hee Yang, Seth Nickerson, Eric T. Kim, Caroline Liot, Gaelle Laurent, Robert Spang, Mark R. Philips, Yibing Shan, David E. Shaw, Dafna Bar‑Sagi, Marcia C. Haigis, and Kevin M. Haigis, “Regulation of RAS Oncogenicity by Acetylation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 27, 2012, pp. 10843–10848. Text
  • Edmond Chow, John L. Klepeis, Charles A. Rendleman, Ron O. Dror, and David E. Shaw, “New Technologies for Molecular Dynamics Simulations,” in Comprehensive Biophysics, Elsevier: Amsterdam, NL, vol. 9, 2012, pp. 86–104. Text
  • Rajintha M. Bandaranayake, Daniela Ungureanu, Yibing Shan, David E. Shaw, Olli Silvennoinen, and Stevan R. Hubbard, “Crystal Structures of the JAK2 Pseudokinase Domain and the Pathogenic Mutant V617F,” Nature Structural & Molecular Biology, vol. 19, no. 8, 2012, pp. 754–759. Text
  • 2011
  • Kresten Lindorff‑Larsen, Stefano Piana, Ron O. Dror, and David E. Shaw, “How Fast‑Folding Proteins Fold,” Science, vol. 334, no. 6055, 2011, pp. 517–520. Text
  • John K. Salmon, Mark A. Moraes, Ron O. Dror, and David E. Shaw, “Parallel Random Numbers: As Easy as 1, 2, 3,” Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC11), New York, NY: ACM, 2011. Text
    Best Paper Award.
  • Ron O. Dror, Daniel H. Arlow, Paul Maragakis, Thomas J. Mildorf, Albert C. Pan, Huafeng Xu, David W. Borhani, and David E. Shaw, “Activation Mechanism of the β2‑Adrenergic Receptor,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 46, 2011, pp. 18684–18689. Text
  • Ron O. Dror, Albert C. Pan, Daniel H. Arlow, David W. Borhani, Paul Maragakis, Yibing Shan, Huafeng Xu, and David E. Shaw, “Pathway and Mechanism of Drug Binding to G‑Protein‑Coupled Receptors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 32, 2011, pp. 13118–13123. Text
  • Yibing Shan, Eric T. Kim, Michael P. Eastwood, Ron O. Dror, Markus A. Seeliger, and David E. Shaw, “How Does a Drug Molecule Find Its Target Binding Site?” Journal of the American Chemical Society, vol. 133, no. 24, 2011, pp. 9181–9183. Text
  • Ron O. Dror, Cliff Young, and David E. Shaw, “Anton, a Special‑Purpose Molecular Simulation Machine,” Encyclopedia of Parallel Computing, New York: Springer, 2011, pp. 60–71. Text
  • Stefano Piana, Kresten Lindorff‑Larsen, and David E. Shaw, “How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?” Biophysical Journal, vol. 100, no. 9, 2011, pp. L47–L49. Text
  • J. Adam Butts, Ping Tak Peter Tang, Ron O. Dror, and David 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 2011 (ARITH20), Tübingen, Germany: IEEE Computer Society, 2011, pp. 149–158. Text
  • Ping Tak Peter Tang, J. Adam Butts, Ron O. Dror, and David 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 2011 (ARITH20), Tübingen, Germany: IEEE Computer Society, 2011, pp. 159–168. Text
  • 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 S. Kuskin, Richard H. Larson, Mark A. Moraes, and David E. Shaw, “Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation,” IEEE Micro, vol. 31, no. 3, 2011, pp. 8–19. Text
  • Daniel M. Rosenbaum, Cheng Zhang, Joseph A. Lyons, Ralph Holl, David Aragao, Daniel H. Arlow, Søren G. F. Rasmussen, Hee‑Jung Choi, Brian T. DeVree, Roger K. Sunahara, Pil Seok Chae, Samuel H. Gellman, Ron O. Dror, David E. Shaw, William I. Weis, Martin Caffrey, Peter Gmeiner, and Brian K. Kobilka, “Structure and Function of an Irreversible Agonist‑β2 Adrenoceptor Complex,” Nature, vol. 469, no. 7329, 2011, pp. 236–240. Text
  • Stefano Piana, Krishnarjun Sarkar, Kresten Lindorff‑Larsen, Minghao Guo, Martin Gruebele, and David E. Shaw, “Computational Design and Experimental Testing of the Fastest‑Folding β‑Sheet Protein,” Journal of Molecular Biology, vol. 405, no. 1, 2011, pp. 43–48. Text
  • Ron O. Dror, Albert C. Pan, Daniel H. Arlow, and David E. Shaw, “Probing the Conformational Dynamics of GPCRs with Molecular Dynamics Simulation,” in G Protein–Coupled Receptors: From Structure to Function, RSC: Cambridge, UK, 2011, pp. 384–400. Text
  • 2010
  • David E. Shaw, Paul Maragakis, Kresten Lindorff‑Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers, “Atomic‑Level Characterization of the Structural Dynamics of Proteins,” Science, vol. 330, no. 6002, 2010, pp. 341–346. Text
  • Morten Ø. Jensen, David W. Borhani, Kresten Lindorff‑Larsen, Paul Maragakis, Vishwanath Jogini, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, “Principles of Conduction and Hydrophobic Gating in K+ Channels,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 13, 2010, pp. 5833–5838. Text
  • 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 S. Kuskin, Richard H. Larson, Mark A. Moraes, and David 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 York, NY: IEEE, 2010. Text
    Best Paper Award Finalist.
  • Ron O. Dror, Morten Ø. Jensen, David W. Borhani, and David E. Shaw, “Exploring Atomic Resolution Physiology on a Femtosecond to Millisecond Timescale Using Molecular Dynamics Simulations,” The Journal of General Physiology, vol. 135, no. 6, 2010, pp. 555–562. Text
  • Michael P. Eastwood, Kate A. Stafford, Ross A. Lippert, Morten Ø. Jensen, Paul Maragakis, Cristian Predescu, Ron O. Dror, and David E. Shaw, “Equipartition and the Calculation of Temperature in Biomolecular Simulations,” Journal of Chemical Theory and Computation, vol. 6, no. 7, 2010, pp. 2045–2058. Text
  • Kresten Lindorff‑Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw, “Improved Side‑Chain Torsion Potentials for the Amber ff99SB Protein Force Field,” Proteins: Structure, Function, and Bioinformatics, vol. 78, no. 8, 2010, pp. 1950–1958. Text
  • Tiankai Tu, Charles A. Rendleman, Patrick J. Miller, Federico Sacerdoti, Ron O. Dror, and David E. Shaw, “Accelerating Parallel Analysis of Scientific Simulation Data via Zazen,” Proceedings of the 8th USENIX Conference on File and Storage Technologies (FAST ’10), Berkeley, CA: USENIX Association, 2010. Text
  • Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw, “Improved Twiddle Access for Fast Fourier Transforms,” IEEE Transactions on Signal Processing, vol. 58, no. 3, 2010, pp. 1122–1130. Text
  • 2009
  • 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, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff‑Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles, “Millisecond‑Scale Molecular Dynamics Simulations on Anton,” Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY: ACM, 2009. Text
    Gordon Bell Prize; Best Paper Award.
  • Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, and David 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 United States of America, vol. 106, no. 12, 2009, pp. 4689–4694. Text
  • Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, Filipp Frank, Huafeng Xu, Morten Ø. Jensen, Ron O. Dror, John Kuriyan, and David 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, vol. 106, no. 1, 2009, pp. 139–144. Text
  • Daniel K. Shenfeld, Huafeng Xu, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, “Minimizing Thermodynamic Length to Select Intermediate States for Free‑Energy Calculations and Replica‑Exchange Simulations,” Physical Review E, vol. 80, no. 4, 2009, pp. 046705‑1–046705‑4. Text
  • Markus A. Seeliger, Pratistha Ranjitkar, Corynn Kasap, Yibing Shan, David E. Shaw, Neil P. Shah, John Kuriyan, and Dustin J. Maly, “Equally Potent Inhibition of c‑Src and Abl by Compounds that Recognize Inactive Kinase Conformations,” Cancer Research, vol. 69, no. 6, 2009, pp. 2384–2392. Text
  • Natalia Jura, Yibing Shan, Xiaoxian Cao, David E. Shaw, and John Kuriyan, “Structural Analysis of the Catalytically Inactive Kinase Domain of the Human EGF Receptor 3,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 51, 2009, pp. 21608–21613. Text
  • Cliff Young, Joseph A. Bank, Ron O. Dror, J.P. Grossman, John K. Salmon, and David E. Shaw, “A 32×32×32, Spatially Distributed 3D FFT in Four Microseconds on Anton,” Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY: ACM, 2009. Text
  • C. Richard Ho, Michael Theobald, Brannon Batson, J.P. Grossman, Stanley C. Wang, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, “Post‑Silicon Debug Using Formal Verification Waypoints,” Proceedings of the Design and Verification Conference and Exhibition (DVCon ’09), San Jose, California, February 24–26, 2009. Text
  • John L. Klepeis, Kresten Lindorff‑Larsen, Ron O. Dror, and David E. Shaw, “Long‑Timescale Molecular Dynamics Simulations of Protein Structure and Function,” Current Opinion in Structural Biology, vol. 19, no. 2, 2009, pp. 120–127. Text
  • Willy Wriggers, Kate A. Stafford, Yibing Shan, Stefano Piana, Paul Maragakis, Kresten Lindorff‑Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, “Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations,” Journal of Chemical Theory and Computation, vol. 5, no. 10, 2009, pp. 2595–2605. Text
  • 2008
  • Morten Ø. Jensen, Ron O. Dror, Huafeng Xu, David W. Borhani, Isaiah T. Arkin, Michael P. Eastwood, and David 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 United States of America, vol. 105, no. 38, 2008, pp. 14430–14435. Text
  • Paul Maragakis, Kresten Lindorff‑Larsen, Michael P. Eastwood, Ron O. Dror, John L. Klepeis, Isaiah T. Arkin, Morten Ø. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arthur G. Palmer III, and David E. Shaw, “Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins,” Journal of Physical Chemistry B, vol. 112, no. 19, 2008, pp. 6155–6158. Text
  • David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. 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, Douglas J. 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, and Stanley C. Wang, “Anton, A Special‑Purpose Machine for Molecular Dynamics Simulation,” Communications of the ACM, vol. 51, no. 7, 2008, pp. 91–97. Text
  • Tiankai Tu, Charles A. Rendleman, David W. Borhani, Ron O. Dror, Justin Gullingsrud, Morten Ø. Jensen, John L. Klepeis, Paul Maragakis, Patrick Miller, Kate A. Stafford, and David E. Shaw, “A Scalable Parallel Framework for Analyzing Terascale Molecular Dynamics Simulation Trajectories,” Proceedings of the ACM/IEEE Conference on Supercomputing (SC08), New York, NY: IEEE, 2008. Text
    Best Paper Award Finalist.
  • Jeffrey S. Kuskin, Cliff Young, J.P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, “Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation,” Proceedings of the 14th Annual International Symposium on High‑Performance Computer Architecture (HPCA ’08), New York, NY: IEEE, 2008. Text
  • Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J.P. Grossman, Yibing Shan, John L. Klepeis, and David E. Shaw, “High‑Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation,” Proceedings of the 14th Annual International Symposium on High‑Performance Computer Architecture (HPCA ’08), New York, NY: IEEE, 2008. Text
  • J.P. Grossman, John K. Salmon, C. Richard Ho, Douglas J. Ierardi, Brian Towles, Brannon Batson, Jochen Spengler, Stanley  C. Wang, Rolf Mueller, Michael Theobald, Cliff Young, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, and David 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), New York, NY: IEEE, 2008. Text
  • C. Richard Ho, Michael Theobald, Martin M. Deneroff, Ron O. Dror, Joseph Gagliardo, and David 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, June 9–13, 2008. Text
  • J.P. Grossman, Cliff Young, Joseph A. Bank, Kenneth Mackenzie, Douglas J. Ierardi, John K. Salmon, Ron O. Dror, and David 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), New York, NY: ACM, 2008. Text
  • 2007
  • Isaiah T. Arkin, Huafeng Xu, Morten Ø. Jensen, Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman‑Tene, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Yibing Shan, and David E. Shaw, “Mechanism of Na+/H+ Antiporting,” Science, vol. 317, no. 5839, 2007, pp. 799–803. Text
  • David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. 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, Douglas J. 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, and Stanley C. Wang, “Anton: A Special‑Purpose Machine for Molecular Dynamics Simulation,” Proceedings of the 34th Annual International Symposium on Computer Architecture (ISCA ’07), New York, NY: ACM, 2007. Text
  • Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, and David E. Shaw, “A Common, Avoidable Source of Error in Molecular Dynamics Integrators,” Journal of Chemical Physics, vol. 126, no. 4, 2007, 046101Text
  • Kevin J. Bowers, Ron O. Dror, and David E. Shaw, “Zonal Methods for the Parallel Execution of Range‑Limited N‑Body Simulations,” Journal of Computational Physics, vol. 221, no. 1, 2007, pp. 303–329. Text
  • 2006
  • Kevin J. Bowers, Ron O. Dror, and David E. Shaw, “The Midpoint Method for Parallelization of Particle Simulations,” Journal of Chemical Physics, vol. 124, no. 18, 2006, 184109Text
  • 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, and David E. Shaw, “Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,” Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), New York, NY: IEEE, 2006.  Text
    Best Paper Award.
  • 2005
  • David E. Shaw, “A Fast, Scalable Method for the Parallel Evaluation of Distance‑Limited Pairwise Particle Interactions,” Journal of Computational Chemistry, vol. 26, no. 13, 2005, pp. 1318–1328. Text
  • Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw, “Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation,” Journal of Chemical Physics, vol. 122, no. 5, 2005, 054101Text
  • Technical Reports
  • Michael Bergdorf, Avi Robinson‑Mosher, Xinyi Guo, Ka‑Hei Law, and David E. Shaw, “Desmond/GPU Performance as of April 2021,” D. E. Shaw Research Technical Report DESRES/TR‑‑2021‑01, April 2021. Text, structure files, and configuration files.
  • Michael Bergdorf, Sean Baxter, Charles A. Rendleman, and David E. Shaw, “Desmond/GPU Performance as of November 2016,” D. E. Shaw Research Technical Report DESRES/TR‑‑2016‑01, November 2016. Text and supplemental information.
  • Michael Bergdorf, Sean Baxter, Charles A. Rendleman, and David E. Shaw, “Desmond/GPU Performance as of October 2015,” D. E. Shaw Research Technical Report DESRES/TR‑‑2015‑01, October 2015. Text and supplemental information.
  • Michael Bergdorf, Eric T. Kim, Charles A. Rendleman, and David E. Shaw, “Desmond/GPU Performance as of November 2014,” D. E. Shaw Research Technical Report DESRES/TR‑‑2014‑01, November 2014. Text and supplemental information.
  • Edmond Chow, Charles A. Rendleman, Kevin J. Bowers, Ron O. Dror, Douglas H. Hughes, Justin Gullingsrud, Federico D. Sacerdoti, and David E. Shaw, “Desmond Performance on a Cluster of Multicore Processors,” D. E. Shaw Research Technical Report DESRES/TR‑‑2008‑01, July 2008. Text