Publications

2024

• J.M. Paggi, A. Pandit, and R.O. Dror. The Art and Science of Molecular Docking. Annual Review of Biochemistry 93, 389-410 (2024). [Link]


• N. Hoppe, S. Harrison, S.H. Hwang, Z. Chen, M. Karelina, I. Deshpande, C.M. Suomivuori, V.R. Palicharla, S.P. Berry, P. Tschaikner, D. Regele, D.F. Covey, E. Stefan, D.S. Marks, J.F. Reitner, R.O. Dror, A.S. Evers, S. Mukhopadhyay, and A. Manglik. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature Structural & Molecular Biology 31, 667–677 (2024). [Link]


• M. Xu, T. Neelands, A.S. Powers, Y. Liu, S.D. Miller, G. Pintilie, J.D. Bois, R.O. Dror, W. Chiu, and M. Maduke. CryoEM structures of the human CLC-2 voltage gated chloride channel reveal a ball and chain gating mechanism. eLife 12:RP90648 (2024). [Link]


• R.S. Ople, N. Ramos-Gonzalez, Q. Li, B.L. Sobecks, D. Aydin, A.S. Powers, A. Faouzi, B.J. Polacco, S.M. Bernhard, K. Appourchaux, S. Sribhashyam, S.O. Eans, B.A. Tsai, R.O. Dror, B.R. Varga, H. Wang, R. Hüttenhain, J.P. McLaughlin, and S. Majumdar. Signaling Modulation Mediated by Ligand Water Interactions with the Sodium Site at μOR. ACS Central Science (2024) [Link]

2023

• A.S. Powers, H.H. Yu, P. Suriana, R.V. Koodli, T. Lu, J.M. Paggi, and R.O. Dror. Geometric Deep Learning for Structure-Based Ligand Design. ACS Central Science 9(12), 2257-2267 (2023). [Link]
  Code and models available on Github


• S. Tajima, Y.S. Kim, M. Fukuda, Y.J. Jo, P.Y. Wang, J.M. Paggi, M. Inoue, E.F.X. Byrne, K.E. Kishi, S. Nakamura, C. Ramakrishnan, S. Takaramoto, T. Nagata, M. Konno, M. Sugiura, K. Katayama, T.E. Matsui, K. Yamashita, S. Kim, H. Ikeda, J. Kim, H. Kandori, R.O. Dror, K. Inoue, K. Deisseroth, and H.E. Kato. Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell 186(20), 4325-4344.e26 (2023). [Link]


• M. Karelina, J.J. Noh, R.O. Dror. How accurately can one predict drug binding modes using AlphaFold models? eLife 12:RP89386 (2023). [Link]
  Media Coverage and Commentary: Science


• W.A. Burger, V. Pham, Z. Vuckovic, A.S. Powers, J.I. Mobbs, Y. Laloudakis, A. Glukhova, D. Wootten, A.B. Tobin, P.M. Sexton, S.M. Paul, C.C. Felder, R. Radostin, R.O. Dror, A. Christopoulos, C. Valant, and D.M. Thal. Xanomeline displays concomitant orthosteric and allosteric binding modes at the M4 mAChR. Nature Communications, 14(1), 5440 (2023). [Link]


• M. Xu, A.S. Powers, R.O. Dror, S. Ermon, J. Leskovec. Geometric Latent Diffusion Models for 3D Molecular Generation. Proceedings of International Conference on Machine Learning (ICML) (2023). [Link]


• S.W. Evans, D.Q. Shi, M. Chavarha, M.H. Plitt, J. Taxidis, B. Madruga, J.L. Fan, F.J. Hwyang, S.C. van Keulen, C.M. Suomivuori, M.M. Pang, S. Su, S. Lee, Y.A. Hao, G. Zhang, D. Jiang, L. Pradhan, R.H. Roth, Y. Liu, C.C. Dorian, A.L. Reese, A. Negrean, A. Losonczy, C.D. Makinson, S. Wang, T.R. Clandinin, R.O. Dror, J.B. Ding, N. Ji, P. Golshani, L.M. Giocomo, G.Q. Bi, and M.Z. Lin. A positively tuned voltage indicator for extended electrical recordings in the brain. Nature Methods 20, 1104-1113 (2023). [Link]


• A.S. Powers, A. Khan, J.M. Paggi, N.R. Latorraca, S. Souza, J.D. Salvo, J. Lu, S.M. Soisson, J.M. Johnston, A.B. Weinglass, and R.O. Dror. A non-canonical mechanism of GPCR activation. bioRxiv preprint (2023). [Link]


• P. Suriana, J.M. Paggi, and R.O. Dror. FlexVDW: A machine learning approach to account for protein flexibility in ligand docking. Proceedings of the Workshop on Machine Learning for Drug Design at the International Conference on Learning Representations (ICLR) (2023). [Link]


• S. Eismann, P. Suriana, B. Jing, R.J.L. Townshend, and R.O. Dror. Protein model quality assessment using rotation-equivariant transformations on point clouds. Proteins 91(8), 1089-1096 (2023). [Link, Code]


• X. Xu, J. Shonberg, J. Kaindl, M.J. Clark, A. Stößel, L. Maul, D. Mayer, H. Hübner, K. Hirata, A.J. Venkatakrishnan, R.O. Dror, B.K. Kobilka, R.K. Sunahara, X. Liu and P. Gmeiner. Constrained catecholamines gain β2AR selectivity through allosteric effects on pocket dynamics. Nature Communications 14, 2138 (2023). [Link]


• K.K. Kumar, M.J. Robertson, E. Thadhani, H. Wang, C.M. Suomivuori, A.S. Powers, L. Ji, S.P. Nikas, R.O. Dror, A. Inoue, A. Makriyannis, G. Skiniotis and B. Kobilka. Structural basis for activation of CB1 by an endocannabinoid analog. Nature Communications 14, 2672 (2023). [Link]


• A.S. Powers, V. Pham, W.A. C. Burger, G. Thompson, Y. Laloudakis, P.M. Sexton, S.M. Paul, A. Christopoulos, D.M. Thal, C.C. Felder, C. Valant and R.O. Dror. Structural basis of efficacy-driven ligand selectivity at GPCRs. Nature Chemical Biology 19, 805-814 (2023). [Link]


• A.E. Daibani, J.M. Paggi, K. Kim, Y.D. Laloudakis, P. Popov, S.M. Bernhard, B.E. Krumm, R.H.J. Olsen, J. Diberto, F.I. Carroll, V. Katritch, B. Wünsch, R.O. Dror and T. Che. Molecular mechanism of biased signaling at the kappa opioid receptor. Nature Communications 14, 1338 (2023). [Link]

2022

• Q. Qu, W. Huang, D. Aydin, J.M. Paggi, A.B. Seven, H. Wang, S. Chakraborty, T. Che, J.F. DiBerto, M.J. Robertson, A. Inoue, C.-M, Suomivuori, B.L. Roth, S. Majumdar, R.O. Dror, B.K. Kobilka and G. Skiniotis. Insights into distinct signaling profiles of the µOR activated by diverse agonists. Nature Chemical Biology 19, 423-430 (2022). [Link]


• B. Faust, C.B. Billesbølle, C.-M. Suomivuori, I. Singh, K. Zhang, N. Hoppe, A.F.M. Pinto, J.K. Diedrich, Y. Muftuoglu, M.W. Szkudlinski, A. Saghatelian, R.O. Dror, Y. Cheng, and A. Manglik. Autoantibody mimicry of hormone action at the thyrotropin receptor. Nature 609, 846-853 (2022). [Link]


• D.D. Liu, L. Melo, A. Costa, M. Vogele, R.J.L. Townshend, and R.O. Dror. Euclidean Transformers for Macromolecular Structures: Lessons Learned. Proceedings of the Workshop on Computational Biology at the International Conference on Machine Learning (ICML) (2022). [Link]


• C. Cao, X. Barros-Álvarez, S. Zhang, K. Kim, M.A. Dämgen, O. Panova, C.-M. Suomivuori, J.F. Fay, X. Zhong, B.E. Krumm, R.H. Gumpper, A.B. Seven, M.J. Robertson, N.J. Krogan, R. Hüttenhain, D.E. Nichols, R.O. Dror, G. Skiniotis, and B.L. Roth. Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD. Neuron 110(19), 3154-3167.E7 (2022). [Link]


• A.S. Powers, H. Yu, P. Suriana, and R.O. Dror. Fragment-Based Ligand Generation Guided By Geometric Deep Learning On Protein-Ligand Structure. Proceedings of the Workshop on Machine Learning for Drug Design at the International Conference on Learning Representations (ICLR) (2022). [Link]


• K. Zhang, N. Horikoshi, S. Li, A.S. Powers, M.A. Hameedi, G.D. Pintilie, H.-D. Chae, Y.A. Khan, C.-M. Suomivuori, R.O. Dror, K.M. Sakamoto, W. Chiu, and S. Wakatsuki. Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia. ACS Central Science 8(2), 214–222 (2022). [Link]


• K.E. Kishi, Y.S. Kim, M. Fukuda, M. Inoue, T. Kusakizako, P.Y. Wang, C. Ramakrishnan, E.F. Byrne, E. Thadhani, J.M. Paggi, T.E. Matsui, K. Yamashita, T., M. Shibata, N, Nomura, S. Iwata, O. Nureki, R.O. Dror, K. Inoue, K. Deisseroth, and H.E. Kato. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell 185(4), 672-689 (2022) [Link]


• N. Tsutsumi, S. Maeda, Q. Qu, M. Vögele, K.M. Jude, C.-M. Suomivuori, O. Panova, D. Waghray, H.E. Kato, A. Velasco, R.O. Dror, G. Skiniotis, B.K. Kobilka, and K.C. Garcia. Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins. Science Advances 8(3), eabl5442 (2022). [Link]


• L. Han, Q. Qu, D. Aydin, O. Panova, M.J. Robertson, Y. Xu, R.O. Dror, G. Skiniotis, and L. Feng. Structure and mechanism of the SGLT family of glucose transporters. Nature 601(7892), 274-279 (2022). [Link]


• J.A. Harris, B. Faust, A.B. Gondin, M.A. Dämgen, C.-M. Suomivuori, N.A. Veldhuis, Y. Cheng, R.O. Dror, D.M. Thal, and A. Manglik. Selective G protein signaling driven by substance P–neurokinin receptor dynamics. Nature Chemical Biology 18(1), 109-115 (2022). [Link]

2021

• R.J.L. Townshend, S. Eismann, A.M. Watkins, R. Rangan, M. Karelina, R. Das, and R.O. Dror. Geometric deep learning of RNA structure. Science 373(6558), 1047-1051 (2021). [Link]


• J.M. Paggi, J.A. Belk, S.A. Hollingsworth, N. Villanueva, A.S. Powers, M.J. Clark, A.G. Chemparathy, J.E. Tynan, T.K. Lau, R.K. Sunahara, and R.O. Dror. Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes. Proceedings of the National Academy of Sciences of the United States of America 118(51), e2112621118 (2021). [Link]


• R.J.L. Townshend, M. Vögele, P. Suriana, A. Derry, A.S. Powers, Y. Laloudakis, S. Balachandar, B. Anderson, S. Eismann, R. Kondor, R.B. Altman, and R.O. Dror. ATOM3D: Tasks On Molecules in Three Dimensions. Advances in Neural Information Processing Systems Datasets and Benchmarks (NeurIPS) (2021). [Link]
  Best Paper Award


• C.A.P. Wood, J. Zhang, D. Aydin, Y. Xu, B.J. Andreone, U.H. Langen, R.O. Dror, C. Gu, and L. Feng. Structure and mechanism of blood–brain-barrier lipid transporter MFSD2A. Nature 596, 444–448 (2021). [Link]


• B. Kelly, S.A. Hollingsworth, D.C. Blakemore, R.M. Owen, R.I. Storer, N.A. Swain, D. Aydin, R. Torella, J.S. Warmus, and R.O. Dror. Delineating the Ligand–Receptor Interactions That Lead to Biased Signaling at the μ-Opioid Receptor. J. Chem. Inf. Model. 61(7), 3696–3707 (2021). [Link]


• B. Jing, S. Eismann, P. Suriana, R.J.L. Townshend, and R.O. Dror. Learning from Protein Structure with Geometric Vector Perceptrons. Proceedings of International Conference of Learning Representations (ICLR) (2021). [PDF] [Open Review]


• A.L. Sanborn, B.T. Yeh, J.T. Feigerle, C.V. Hao, R.J.L. Townshend, E.L. Aiden, R.O. Dror, and R.D Kornberg. Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. eLife 10:e68068 (2021). [Link]


• M. Jagota, R.J.L. Townshend, L. Kang, D.A. Bushnell, R.O. Dror, R.D. Kornberg, and M. Azubel. Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy. Ultramicroscopy 227, 113302 (2021). [Link]


• K.E. Komolov, S.M. Sulon, A. Bhardwaj, S.C. van Keulen, N.M. Duc, D.K. Laurinavichyute, H.J. Lou, B.E. Turk, K.Y. Chung, R.O. Dror, and J.L. Benovic. Structure of a GRK5-calmodulin complex reveals molecular mechanism of GRK activation and substrate targeting. Molecular Cell 81(2), 323-339 (2021). [Link]

2020

• C.-M. Suomivuori, N.R. Latorraca, L.M. Wingler, S. Eismann, M.C. King, A.W. Kleinhenz, M.A. Skiba, D.P. Staus, A.C. Kruse, R.J. Lefkowitz, and R.O. Dror. Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor. Science 367(6480), 881-887 (2020). [Link]
  Media Coverage and Commentary: AAAS EurekAlert! , HPC wire , Stanford Engineering Magazine


• N.R. Latorraca, M. Masureel, S.A. Hollingsworth, F.M. Heydenreich, C.-M. Suomivuori, C. Brinton, R.J.L. Townshend, M. Bouvier, B.K. Kobilka, and R.O. Dror. How GPCR Phosphorylation Patterns Orchestrate Arrestin-Mediated Signaling. Cell 183(7), 1813-1825 (2020). [Link]


• S. Eismann, R.J.L. Townshend, N. Thomas, M. Jagota, B. Jing, and R.O. Dror. Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes. Proteins 89(5), 493-501 (2020). [Link]


• E.M. Jones, N.B. Lubock, A.J. Venkatakrishnan, J. Wang, A.M. Tseng, J.M. Paggi, N.R. Latorraca, D. Cancilla, M. Satyadi, J.E. Davis, M.M. Babu, R.O. Dror, and S. Kosuri. Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning. eLife 9:e54895 (2020). [Link]


• L.M. Wingler, M.A. Skiba, C. McMahon, D.P. Staus, A.W. Kleinhenz, C.-M. Suomivuori, N.R. Latorraca, R.O. Dror., R.J. Lefkowitz, and A.C. Kruse. Angiotensin and biased analogs induce structurally distinct active conformations within a GPCR. Science 367(6480), 888-892 (2020). [Link]


• C.B. Billesbølle, C.M. Azumaya, R.C. Kretsch, A.S. Powers, S. Gonen, S. Schneider, T. Arvedson, R.O. Dror, Y. Cheng, and A. Manglik. Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms. Nature 586, 807–811 (2020). [Link]


• R.J.L. Townshend, B. Townshend, S. Eismann, and R.O. Dror. Geometric Prediction: Moving Beyond Scalars. arXiv preprint. [Link]

2019

• R.J.L. Townshend, R. Bedi, P. Suriana, and R.O. Dror. End-to-End Learning on 3D Protein Structure for Interface Prediction. NeurIPS 2019. [Link]


• T.A. Chew, B.J. Orlando, J. Zhang, N.R. Latorraca, A. Wang, S.A. Hollingsworth, D.H. Chen, R.O. Dror, M. Liao and L. Feng. Structure and mechanism of the cation–chloride cotransporter NKCC1. Nature 572:488–492 (2019). [Link]


• S.A. Hollingsworth, B. Kelly, C. Valant, J.A. Michaelis, O. Mastromihalis, G. Thompson, A.J. Venkatakrishnan, S. Hertig, P.J. Scammells, P.M. Sexton, C.C. Felder, A. Christopoulos and R.O. Dror. Cryptic pocket formation underlies allosteric modulator selectivity at muscarinic GPCRs. Nature Communications 10:3289 (2019). [Link]


• H.E. Kato, Y. Zhang, H. Hu, C.-M. Suomivuori, F.M.N. Kadji, J. Aoki, K.K. Kumar, R. Fonseca, D. Hilger, W. Huang, N. R. Latorraca, A. Inoue, R.O. Dror, B.K. Kobilka and G. Skiniotis. Conformational transitions of a neurotensin receptor 1–Gi1 complex. Nature 572:80–85 (2019). [Link]


• I. Deshpande, J. Liang, D. Hedeen, K.J. Roberts, Y. Zhang, B. Ha, N.R. Latorraca, B. Faust, R.O. Dror, P.A. Beachy, B.R. Myers and A. Manglik. Smoothened stimulation by membrane sterols drives Hedgehog pathway activity. Nature 571:284–288 (2019). [Link]


• A.J. Venkatakrishnan, A. Ma, R. Fonseca, N. Latorraca, B. Kelly, R. Betz, C. Asawa, B. Kobilka, and R.O. Dror. Diverse GPCRs exhibit conserved water networks for stabilization and activation. Proceedings of the National Academy of Sciences of the United States of America 116(8):3288-3293 (2019). [Link]


• R. Betz and R.O. Dror. How effectively can adaptive sampling methods capture spontaneous ligand binding?. Journal of Chemical Theory and Computation 15(3):2053-2063 (2019). [Link]


• L.M. Wingler, E. Matthias, D. Hilger, N.R. Latorraca, M.T. Lerch, D.P. Staus, R.O. Dror, B.K. Kobilka, W.L. Hubbell, and R.J. Lefkowitz. Angiotensin analogs with divergent bias stabilize distinct receptor conformations. Cell 176(3):468-478 (2019). [Link]


• K.K. Kumar, M. Shalev-Benami, M.J. Robertson, H. Hu, S.D. Banister, S.A. Hollingsworth, N.R. Latorraca, H.E. Kato, D. Hilger, S. Maeda, W.I. Weis, D.L. Farrens, R.O. Dror, S.V. Malhotra, B.K. Kobilka, and G. Skiniotis. Structure of a signaling cannabinoid receptor 1-G protein complex. Cell 176(3):448–458 (2019). [Link]

2018

• N.R. Latorraca, J.K. Wang, B. Bauer, R.J.L. Townshend, S.A. Hollingsworth, J.E. Olivieri, H.E. Xu, M.E. Sommer, and R.O. Dror. Molecular mechanism of GPCR-mediated arrestin activation. Nature 557:452-456 (2018). [Link]
  Media Coverage and Commentary: Nature News and Views, Nature Research Highlight, Futurity, Stanford Medicine Scope, Stanford News


• K. Eichel, D. Jullié, B. Barsi-Rhyne, N.R. Latorraca, M. Masureel, J. Sibarita, R.O. Dror, and M. von Zastrow. Catalytic activation of β-arrestin by GPCRs. Nature 557:381-386 (2018). [Link]
  Media Coverage and Commentary: Nature News and Views


• A. Koehl, H. Hu, S. Maeda, Y. Zhang, Q. Qu, J.M. Paggi, N.R. Latorraca, D. Hilger, R. Dawson, H. Matile, G.F.X. Schertler, S. Granier, W.I. Weis, R.O. Dror, A. Manglik, G. Skiniotis, and B.K. Kobilka. Structure of the μ opioid receptor-Gi protein complex. Nature 558:547–552 (2018). [Link]


• H.R. Schmidt, R.M. Betz, R.O. Dror, and A.C. Kruse. Structural basis for sigma-1 receptor ligand recognition. Nature Structural & Molecular Biology 25:981-987 (2018). [Link]
  Media Coverage and Commentary: Nature Structural & Molecular Biology News and Views


• S.A. Hollingsworth and R.O. Dror. Molecular dynamics simulation for all. Neuron 99(6):1129-1143 (2018). [Link]


• H.E. Kato, Y.S. Kim, J.M. Paggi, K.E. Evans, W.E. Allen, C. Richardson, K. Inoue, S. Ito, C. Ramakrishnan, Lief E. Fenno, K. Yamashita, D. Hilger, S.Y. Lee, A. Berndt, K. Shen, H. Kandori, R.O. Dror, B.K. Kobilka, and K. Deisseroth. Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature 561:349–354 (2018). [Link]
  Media Coverage and Commentary: Nature News and Views


• Y.S. Kim, H.E. Kato, K. Yamashita, S. Ito, K. Inoue, C. Ramakrishnan, L.E. Fenno, K.E. Evans, J.M. Paggi, R.O. Dror, H. Kandori, B.K. Kobilka, and K. Deisseroth. Crystal structure of a natural anion-conducting channelrhodopsin GtACR1. Nature 561:343–348 (2018). [Link]
  Media Coverage and Commentary: Nature News and Views


• N. van Eps, C. Altenbach, L.N. Caro, N.R. Latorraca, S.A. Hollingsworth, R.O. Dror, O.P. Ernst, and W.L. Hubbell. Gi- and Gs-coupled GPCRs show different modes of G-protein binding. Proceedings of the National Academy of Sciences of the United States of America 115:2383-2388 (2018). [Link]


• J.D. McCorvy, K.V. Butler, B. Kelly, K. Rechsteiner, J. Karpiak, R.M. Betz, B.L. Kormos, B.K. Shoichet, R.O. Dror, J. Jin, and B.L. Roth. Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. Nature Chemical Biology 14:126–134 (2018). [Link]


• M. Masureel, Y. Zou, L. Picard, E. Westhuizen, J.P. Mahoney, J.P.G.L. Rodrigues, T.J. Mildorf, R.O. Dror, D.E. Shaw, M. Bouvier, E. Pardon, J. Steyaert, R.K. Sunahara, W.I. Weis, C. Zhang, and B.K. Kobilka. Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist. Nature Chemical Biology 14:1059-1066 (2018). [Link]


• M.P. Bokoch, H. Jo, J.R. Valcourt, Y. Srinivasan, A.C. Pan, S. Capponi, M. Grabe, R.O. Dror, D.E. Shaw, W.F. DeGrado, and S.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 57:5748-5758 (2018). [Link]

2017

• S. Wang, D. Wacker, A. Levit, T. Che, R.M. Betz, J.D. McCorvy, A.J. Venkatakrishnan, X.-P. Huang, R.O. Dror, B.K. Shoichet, and B.L. Roth. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science 358: 381–386 (2017). [Link]


• X. Liu, S. Ahn, A.W. Kahsai, K.C. Meng, N.R. Latorraca, B. Pani, A.J. Venkatakrishnan, A. Masoudi, W.I. Weis, R.O. Dror, X. Chen, R.J. Lefkowitz, and B.K. Kobilka. Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure. Nature 548: 480-484 (2017). [Link]


• X.E. Zhou, Y. He, P.W. de Waal, X. Gao, Y. Kang, N. Van Eps, Y. Yin, K. Pal, D. Goswami, T.A. White, A. Barty, N.R. Latorraca, H.N. Chapman, W.L. Hubbell, R.O. Dror, R.C. Stevens, V. Cherezov, V.V. Gurevich, P.R. Griffin, O.P. Ernst, K. Melcher, and H.E. Xu. Identification of phosphorylation codes for arrestin recruitment by G protein-coupled receptors. Cell 170: 457-469 (2017). [Link]


• K.E. Komolov, Y. Du, N.M. Duc, R.M. Betz, J.P.G.L.M. Rodrigues, R.D. Leib, D. Patra, G. Skiniotis, C.M. Adams, R.O. Dror, K.Y. Chung, B.K. Kobilka, and J.L. Benovic. Structural and functional analysis of a β2-Adrenergic receptor complex with GRK5. Cell 169: 407-421 (2017). [Link]


• N.R. Latorraca, N.M. Fastman, A.J. Venkatakrishnan, W.B. Frommer, R.O. Dror, and L. Feng. Mechanism of substrate translocation in an alternating access transporter. Cell 169: 96-107 (2017). [Link]
  Media Coverage and Commentary: Stanford News


• N.R. Latorraca, A.J. Venkatakrishnan, and R.O. Dror. GPCR dynamics: structures in motion. Chemical Reviews 117: 139-155 (2017). [Link]


• D. Wacker, S. Wang, J.D. McCorvy, R.M. Betz, A.J. Venkatakrishnan, A. Levit, K. Lansu, Z.L. Schools, T. Che, D.E. Nichols, B.K. Shoichet, R.O. Dror, and B.L. Roth. Crystal structure of an LSD-Bound human serotonin receptor. Cell 168: 377-389 (2017). [Link]
  Media Coverage and Commentary: Newsweek

2016

• B. Zimmerman, B. Kelly, T. Seegar, B.J. McMillan, R.O. Dror, A.C. Kruse, and S. Blacklow. Crystal structure of a full-length human tetraspanin reveals a cholesterol-binding pocket. Cell 167: 1041–1051 (2016). [Link]


• S. Hertig, N.R. Latorraca, and R.O. Dror. Revealing atomic-level mechanisms of protein allostery with molecular dynamics simulations. PLOS Computational Biology. 12: e1004746 (2016). [Link]


• D. Guo, A.C. Pan, R.O. Dror, T. Mocking, R. Liu, L. Heitman, D.E. Shaw, and A.P. IJzerman. Molecular basis of ligand dissociation from the adenosine A2A receptor. Molecular Pharmacology 89: 485–491 (2016). [Link]

2015

• 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 524: 315–321 (2015). [Link]


• 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). [Link]


• 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). [Link]


• 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). [Link]

2014

• A. Ranganathan, R.O. Dror, J. Carlsson. Insights into the role of Asp792.50 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.

2013

• 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).


• 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).


• 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. 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).


• 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).


• 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).

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).


• 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).


• M.Ø. Jensen, V. Jogini, D.W. Borhani, A.E. Lefler, R.O. Dror, and D.E. Shaw. Mechanism of voltage gating in K+ 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).


• 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).


• 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).


• 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).


• 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).


• E. Chow, J.L. Klepeis, C.A. Rendleman, R.O. Dror, and D.E. Shaw. New technologies for molecular dynamics simulations. In Comprehensive Biophysics, E.H. Egelman, ed., Amsterdam: Elsevier. 9:86–104 (2012).

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).
  
  
• 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 United States of America. 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 United States of America, 108: 13118–13123 (2011).


• 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).


• 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). New York, NY: IEEE (2011). Best Paper Award.


• 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). Washington, DC: IEEE Computer Society (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). Washington, DC: IEEE Computer Society (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).

2010

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


• 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 United States of America, 107: 5833–5838 (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).


• 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, 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 York, NY: IEEE (2010). Best Paper Award Finalist.


• T. Tu, C.A. Rendleman, P. Miller, F. Sacerdoti, R.O. Dror, and D.E. Shaw. Accelerating parallel analysis of scientific simulation data via Zazen. Proceedings of the USENIX Conference on File and Storage Technologies (FAST). Berkeley, CA: USENIX Association (2010).

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: 046705-1–046705-4 (2009).


• W. Wriggers, K.A. Stafford, Y. Shan, S. Piana, P. Maragakis, K. Lindorff-Larsen, P.J. Miller, 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).


• 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 United States of America, 106: 4689–4694 (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).


• 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).


• 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 simulation on Anton. Proceedings of the Conference for High Performance Computing, Networking, Storage and Analysis (SC09). New York, NY: ACM (2009). Gordon Bell Prize; Best Paper Award.


• C. Young, J.A. Bank, R.O. Dror, J.P. Grossman, J.K. Salmon, and D. E. Shaw. A 323232, spatially distributed 3D FFT in five microseconds on Anton. Proceedings of the Conference for High Performance Computing, Networking, Storage and Analysis (SC09). New York, NY: ACM (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 (EMBC). New York, NY: IEEE (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), San Jose (2009).

2008

• 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 United States of America, 105: 14430–14435 (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. Kolossváry, 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).


• 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).


• 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 trajectories. Proceedings of the ACM/IEEE Conference on Supercomputing (SC08). New York, NY: IEEE (2008). Best Paper Award Finalist.


• 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 heterogenous multicore ASICs. Proceedings of the 6th IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES/ISSS). New York, NY: ACM (2008).


• 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). New York, NY: IEEE (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 intrinisically hard-to-verify logic. Proceedings of the 45th Design Automation Conference (DAC), Anaheim (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 (HPCA). New York, NY: IEEE (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 (HPCA). New York, NY: IEEE (2008).

2007

• I.T. Arkin, H. Xu, M.Ø. Jensen, E. Arbely, E.R. Bennett, K.J. Bowers, E. Chow, R.O. Dror, M.P. Eastwood, R. Flitman-Tene, B.A. Gregersen, J.L. Klepeis, I. Kolossváry, Y. Shan, and D.E. Shaw. Mechanism of Na+/H+ antiporting. Science 317: 799–803 (2007).


• R.A. Lippert, K.J. Bowers, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossváry, and D.E. Shaw. A common, avoidable source of error in molecular dynamics integrators. Journal of Chemical Physics 126: 046101 (2007).


• K.J. Bowers, R.O. Dror, and D.E. Shaw. Zonal methods for the parallel execution of range- limited N-body simulations. Journal of Computational Physics 221: 303–329 (2007).


• 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. Kolossváry, 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. Proceedings of the 34rd Annual International Symposium on Computer Architecture (ISCA). New York, NY: ACM (2007).

2006

• K.J. Bowers, R.O. Dror, and D.E. Shaw. The midpoint method for parallelization of particle simulations. Journal of Chemical Physics 124: 184109 (2006).


• K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossváry, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, and D.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). Best Paper Award.

2005

• Y. Shan, J.L. Klepeis, M.P. Eastwood, R.O. Dror, and D.E. Shaw. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. Journal of Chemical Physics 122: 054101 (2005).


• K.J. Bowers, R.O. Dror, and D.E. Shaw. Overview of neutral territory methods for the parallel evaluation of pairwise particle interactions. Proceedings of the Scientific Discovery through Advanced Computing (SciDAC), San Francisco, June 2005. Journal of Physics: Conference Series 16:300–304 (2005).

2004

• R.O. Dror, A.S. Willsky, and E.H. Adelson. Statistical characterization of real-world illumination. Journal of Vision 4: 821–837 (2004).

2003

• R.O. Dror, J.G. Murnick, N.J. Rinaldi, V.D. Marinescu, R.M. Rifkin, and R.A. Young. Bayesian estimation of transcript levels using a general model of array measurement noise. Journal of Computational Biology 10: 433–452 (2003).


• R.W. Fleming, R.O. Dror, and E.H. Adelson. Real-world illumination and the perception of surface reflectance properties. Journal of Vision 3: 347–368 (2003).

2002

• R.O. Dror, J.G. Murnick, N.J. Rinaldi, V.D. Marinescu, R.M. Rifkin, and R.A. Young. A Bayesian approach to transcript estimation from gene array data: The BEAM technique. Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC (2002).

2001

• R.O. Dror, T.K. Leung, E.H. Adelson, and A.S. Willsky. Statistics of real-world illumination. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Hawaii (2001).


• R.O. Dror, E.H. Adelson, and A.S. Willsky. Recognition of surface reflectance properties from a single image under unknown real-world illumination. Proceedings of the Workshop on Identifying Objects Across Variations in Lighting at the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Hawaii (2001).


• R.W. Fleming, R.O. Dror, and E.H. Adelson. How do humans determine reflectance properties under unknown illumination? Proceedings of the Workshop on Identifying Objects Across Variations in Lighting at the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Hawaii (2001).


• R.O. Dror, E.H. Adelson, and A.S. Willsky. Surface reflectance estimation and natural illumination statistics. Proceedings of the Second International Workshop on Statistical and Computational Theories of Vision at the IEEE International Conference on Computer Vision (ICCV), Vancouver (2001).


• R.O. Dror, E.H. Adelson, and A.S. Willsky. Estimating surface reflectance properties from images under unknown illumination. Proceedings of SPIE 4299: Human Vision and Electronic Imaging VI (HVEI), San Jose (2001).


• R.O. Dror, D.C. O’Carroll, and S.B. Laughlin. Accuracy of velocity estimation by Reichardt correlators. Journal of the Optical Society of America A 18: 241–252 (2001).

2000

• R.O. Dror, D.C. O’Carroll, and S.B. Laughlin. The role of natural image statistics in biological motion estimation. IEEE International Workshop on Biologically Motivated Computer Vision (BMCV), Seoul (2000). Lecture Notes in Computer Science 1811: 492–501 (2000).

1999

• R.O. Dror, C.C. Canavier, R.J. Butera, J.W. Clark, and J.H. Byrne. A mathematical criterion based on phase response curves for stability in a ring of coupled oscillators. Biological Cybernetics 80: 11–23 (1999).

1997

• C.C. Canavier, R.J. Butera, R.O. Dror, D.A. Baxter, J.W. Clark, and J.H. Byrne. Phase response characteristics of model neurons determine which patterns are expressed in a ring circuit model of gait generation. Biological Cybernetics 77: 367–380 (1997).

1996

• R.O. Dror, S. Ganguli, and R.S. Strichartz. A search for best constants in the Hardy- Littlewood maximal theorem. Journal of Fourier Analysis and Applications 2: 473–86 (1996).