David Elliot Shaw - Publications

Affiliations: 
D. E. Shaw Research, New York, NY, United States 
Area:
computational biochemistry
Website:
http://www.deshaw.com/Founder.shtml

155 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Wang Q, Pechersky Y, Sagawa S, Pan AC, Shaw DE. 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. PMID 31019091 DOI: 10.1073/pnas.1819301116  0.6
2019 Pan AC, Jacobson D, Yatsenko K, Sritharan D, Weinreich TM, Shaw DE. Atomic-level characterization of protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. PMID 30760596 DOI: 10.1073/pnas.1815431116  0.6
2018 Masureel M, Zou Y, Picard LP, van der Westhuizen E, Mahoney JP, Rodrigues JPGLM, Mildorf TJ, Dror RO, Shaw DE, Bouvier M, Pardon E, Steyaert J, Sunahara RK, Weis WI, Zhang C, et al. Publisher Correction: Structural insights into binding specificity, efficacy and bias of a βAR partial agonist. Nature Chemical Biology. PMID 30504785 DOI: 10.1038/s41589-018-0182-5  0.36
2018 Zanetti-Domingues LC, Korovesis D, Needham SR, Tynan CJ, Sagawa S, Roberts SK, Kuzmanic A, Ortiz-Zapater E, Jain P, Roovers RC, Lajevardipour A, van Bergen En Henegouwen PMP, Santis G, Clayton AHA, Clarke DT, ... ... Shaw DE, et al. The architecture of EGFR's basal complexes reveals autoinhibition mechanisms in dimers and oligomers. Nature Communications. 9: 4325. PMID 30337523 DOI: 10.1038/s41467-018-06632-0  0.6
2018 Masureel M, Zou Y, Picard LP, van der Westhuizen E, Mahoney JP, Rodrigues JPGLM, Mildorf TJ, Dror RO, Shaw DE, Bouvier M, Pardon E, Steyaert J, Sunahara RK, Weis WI, Zhang C, et al. Structural insights into binding specificity, efficacy and bias of a βAR partial agonist. Nature Chemical Biology. 14: 1059-1066. PMID 30327561 DOI: 10.1038/s41589-018-0145-x  0.36
2018 Piana S, Shaw DE. Atomic-Level Description of Protein Folding inside the GroEL Cavity. The Journal of Physical Chemistry. B. PMID 30277396 DOI: 10.1021/acs.jpcb.8b07366  0.32
2018 Bokoch MP, Jo H, Valcourt JR, Srinivasan Y, Pan AC, Capponi S, Grabe M, Dror RO, Shaw DE, DeGrado WF, Coughlin SR. Entry from the lipid bilayer: a possible pathway for inhibition of a peptide G protein-coupled receptor by a lipophilic small molecule. Biochemistry. PMID 30102523 DOI: 10.1021/acs.biochem.8b00577  0.6
2018 Robustelli P, Piana S, Shaw DE. 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. PMID 29735687 DOI: 10.1073/pnas.1800690115  0.32
2018 Tan D, Piana S, Dirks RM, Shaw DE. 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. PMID 29378935 DOI: 10.1073/pnas.1713027115  0.32
2017 McGibbon RT, Taube AG, Donchev AG, Siva K, Hernández F, Hargus C, Law KH, Klepeis JL, Shaw DE. Improving the accuracy of Møller-Plesset perturbation theory with neural networks. The Journal of Chemical Physics. 147: 161725. PMID 29096510 DOI: 10.1063/1.4986081  0.36
2017 Sangwan S, Zhao A, Adams KL, Jayson CK, Sawaya MR, Guenther EL, Pan AC, Ngo J, Moore DM, Soriaga AB, Do TD, Goldschmidt L, Nelson R, Bowers MT, Koehler CM, ... Shaw DE, et al. 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. PMID 28760994 DOI: 10.1073/pnas.1705091114  0.6
2017 Pan AC, Xu H, Palpant T, Shaw DE. Quantitative characterization of the binding and unbinding of millimolar drug fragments with molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 28582625 DOI: 10.1021/acs.jctc.7b00172  0.6
2016 Needham SR, Roberts SK, Arkhipov A, Mysore VP, Tynan CJ, Zanetti-Domingues LC, Kim ET, Losasso V, Korovesis D, Hirsch M, Rolfe DJ, Clarke DT, Winn MD, Lajevardipour A, Clayton AH, ... ... Shaw DE, et al. EGFR oligomerization organizes kinase-active dimers into competent signalling platforms. Nature Communications. 7: 13307. PMID 27796308 DOI: 10.1038/ncomms13307  0.6
2016 Lindorff-Larsen K, Maragakis P, Piana S, Shaw DE. Picosecond to Millisecond Structural Dynamics in Human Ubiquitin. The Journal of Physical Chemistry. B. PMID 27082121 DOI: 10.1021/acs.jpcb.6b02024  0.32
2016 Guo D, Pan AC, Dror RO, Mocking T, Liu R, Heitman L, Shaw DE, IJzerman AP. Molecular basis of ligand dissociation from the adenosine A2A receptor. Molecular Pharmacology. PMID 26873858 DOI: 10.1124/mol.115.102657  0.36
2016 Pan AC, Weinreich TM, Piana S, Shaw DE. Demonstrating an order-of-magnitude sampling enhancement in molecular dynamics simulations of complex protein systems. Journal of Chemical Theory and Computation. PMID 26866996 DOI: 10.1021/acs.jctc.5b00913  0.6
2016 Xu H, Shaw DE. A Simple Model of Multivalent Adhesion and Its Application to Influenza Infection. Biophysical Journal. 110: 218-233. PMID 26745425 DOI: 10.1016/j.bpj.2015.10.045  0.36
2015 Chung HS, Piana-Agostinetti S, Shaw DE, Eaton WA. Structural origin of slow diffusion in protein folding. Science (New York, N.Y.). 349: 1504-10. PMID 26404828 DOI: 10.1126/science.aab1369  0.36
2015 Ingram JR, Knockenhauer KE, Markus BM, Mandelbaum J, Ramek A, Shan Y, Shaw DE, Schwartz TU, Ploegh HL, Lourido S. Allosteric activation of apicomplexan calcium-dependent protein kinases. Proceedings of the National Academy of Sciences of the United States of America. 112: E4975-84. PMID 26305940 DOI: 10.1073/pnas.1505914112  0.36
2015 Raval A, Piana S, Eastwood MP, Shaw DE. Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations. Protein Science : a Publication of the Protein Society. PMID 26266489 DOI: 10.1002/pro.2770  0.36
2015 Dror RO, Mildorf TJ, Hilger D, Manglik A, Borhani DW, Arlow DH, Philippsen A, Villanueva N, Yang Z, Lerch MT, Hubbell WL, Kobilka BK, Sunahara RK, Shaw DE. SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins. Science (New York, N.Y.). 348: 1361-5. PMID 26089515 DOI: 10.1126/science.aaa5264  0.36
2015 Fan Z, Dror RO, Mildorf TJ, Piana S, Shaw DE. 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: 7454-9. PMID 26025225 DOI: 10.1073/pnas.1415846112  0.36
2015 Sborgi L, Verma A, Piana S, Lindorff-Larsen K, Cerminara M, Santiveri CM, Shaw DE, de Alba E, Muñoz V. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations. Journal of the American Chemical Society. 137: 6506-16. PMID 25924808 DOI: 10.1021/jacs.5b02324  0.36
2015 Piana S, Donchev AG, Robustelli P, Shaw DE. Water dispersion interactions strongly influence simulated structural properties of disordered protein States. The Journal of Physical Chemistry. B. 119: 5113-23. PMID 25764013 DOI: 10.1021/jp508971m  0.36
2015 Foda ZH, Shan Y, Kim ET, Shaw DE, Seeliger MA. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase. Nature Communications. 6: 5939. PMID 25600932 DOI: 10.1038/ncomms6939  0.36
2015 Xu H, Schmidt AG, O'Donnell T, Therkelsen MD, Kepler TB, Moody MA, Haynes BF, Liao HX, Harrison SC, Shaw DE. Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage. Proteins. 83: 771-80. PMID 25524709 DOI: 10.1002/prot.24745  0.36
2015 Fan Z, Dror RO, Mildorf TJ, Piana S, Shaw DE. 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: 1-6. DOI: 10.1073/pnas.1415846112  0.36
2014 Pan AC, Weinreich TM, Shan Y, Scarpazza DP, Shaw DE. 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. 10: 2860-5. PMID 26586510 DOI: 10.1021/ct500223p  0.6
2014 Littlefield P, Liu L, Mysore V, Shan Y, Shaw DE, Jura N. Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations. Science Signaling. 7: ra114. PMID 25468994 DOI: 10.1126/scisignal.2005786  0.36
2014 Kavran JM, McCabe JM, Byrne PO, Connacher MK, Wang Z, Ramek A, Sarabipour S, Shan Y, Shaw DE, Hristova K, Cole PA, Leahy DJ. How IGF-1 activates its receptor. Elife. 3. PMID 25255214 DOI: 10.7554/eLife.03772  0.6
2014 Ferrao R, Zhou H, Shan Y, Liu Q, Li Q, Shaw DE, Li X, Wu H. IRAK4 dimerization and trans-autophosphorylation are induced by Myddosome assembly. Molecular Cell. 55: 891-903. PMID 25201411 DOI: 10.1016/j.molcel.2014.08.006  0.36
2014 Arkhipov A, Shan Y, Kim ET, Shaw DE. Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor. Plos Computational Biology. 10: e1003742. PMID 25058506 DOI: 10.1371/journal.pcbi.1003742  0.36
2014 Shan Y, Gnanasambandan K, Ungureanu D, Kim ET, Hammarén H, Yamashita K, Silvennoinen O, Shaw DE, Hubbard SR. Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase. Nature Structural & Molecular Biology. 21: 579-84. PMID 24918548 DOI: 10.1038/nsmb.2849  0.36
2014 Piana S, Klepeis JL, Shaw DE. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Current Opinion in Structural Biology. 24: 98-105. PMID 24463371 DOI: 10.1016/j.sbi.2013.12.006  0.36
2014 Shaw DE, Grossman JP, Bank JA, Batson B, Butts JA, Chao JC, Deneroff MM, Dror RO, Even A, Fenton CH, Forte A, Gagliardo J, Gill G, Greskamp B, Ho CR, et al. Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer International Conference For High Performance Computing, Networking, Storage and Analysis, Sc. 2015: 41-53. DOI: 10.1109/SC.2014.9  0.36
2014 Towles B, Grossman JP, Greskamp B, Shaw DE. Unifying on-chip and inter-node switching within the Anton 2 network Proceedings - International Symposium On Computer Architecture. 1-12. DOI: 10.1109/ISCA.2014.6853238  0.36
2014 Pan AC, Weinreich TM, Shan Y, Scarpazza DP, Shaw DE. 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. 10: 2860-2865. DOI: 10.1021/ct500223p  0.36
2013 Lippert RA, Predescu C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror RO, Shaw DE. Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure. The Journal of Chemical Physics. 139: 164106. PMID 24182003 DOI: 10.1063/1.4825247  0.36
2013 Dror RO, Green HF, Valant C, Borhani DW, Valcourt JR, Pan AC, Arlow DH, Canals M, Lane JR, Rahmani R, Baell JB, Sexton PM, Christopoulos A, Shaw DE. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature. 503: 295-9. PMID 24121438 DOI: 10.1038/nature12595  0.36
2013 Piana S, Lindorff-Larsen K, Shaw DE. Atomistic description of the folding of a dimeric protein. The Journal of Physical Chemistry. B. 117: 12935-42. PMID 23882999 DOI: 10.1021/jp4020993  0.36
2013 Arkhipov A, Shan Y, Kim ET, Dror RO, Shaw DE. Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family. Elife. 2: e00708. PMID 23878723 DOI: 10.7554/eLife.00708  0.36
2013 Eastwood MP, Chitra T, Jumper JM, Palmo K, Pan AC, Shaw DE. Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment. The Journal of Physical Chemistry. B. 117: 12898-907. PMID 23841719 DOI: 10.1021/jp402102w  0.36
2013 Kim TH, Chung KY, Manglik A, Hansen AL, Dror RO, Mildorf TJ, Shaw DE, Kobilka BK, Prosser RS. The role of ligands on the equilibria between functional states of a G protein-coupled receptor. Journal of the American Chemical Society. 135: 9465-74. PMID 23721409 DOI: 10.1021/ja404305k  0.36
2013 Jensen MØ, Jogini V, Eastwood MP, Shaw DE. Atomic-level simulation of current-voltage relationships in single-file ion channels. The Journal of General Physiology. 141: 619-32. PMID 23589581 DOI: 10.1085/jgp.201210820  0.36
2013 Shan Y, Arkhipov A, Kim ET, Pan AC, Shaw DE. Transitions to catalytically inactive conformations in EGFR kinase. Proceedings of the National Academy of Sciences of the United States of America. 110: 7270-5. PMID 23576739 DOI: 10.1073/pnas.1220843110  0.6
2013 Piana S, Lindorff-Larsen K, Shaw DE. Atomic-level description of ubiquitin folding. Proceedings of the National Academy of Sciences of the United States of America. 110: 5915-20. PMID 23503848 DOI: 10.1073/pnas.1218321110  0.36
2013 Pan AC, Borhani DW, Dror RO, Shaw DE. Molecular determinants of drug-receptor binding kinetics. Drug Discovery Today. 18: 667-73. PMID 23454741 DOI: 10.1016/j.drudis.2013.02.007  0.36
2013 Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, Wemmer DE, Kuriyan J, Shaw DE. Architecture and membrane interactions of the EGF receptor. Cell. 152: 557-69. PMID 23374350 DOI: 10.1016/j.cell.2012.12.030  0.36
2013 Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, Huang Y, Pelton JG, Shan Y, Shaw DE, Wemmer DE, Groves JT, Kuriyan J. Conformational coupling across the plasma membrane in activation of the EGF receptor. Cell. 152: 543-56. PMID 23374349 DOI: 10.1016/j.cell.2012.12.032  0.36
2013 Nygaard R, Zou Y, Dror RO, Mildorf TJ, Arlow DH, Manglik A, Pan AC, Liu CW, Fung JJ, Bokoch MP, Thian FS, Kobilka TS, Shaw DE, Mueller L, Prosser RS, et al. The dynamic process of β(2)-adrenergic receptor activation. Cell. 152: 532-42. PMID 23374348 DOI: 10.1016/j.cell.2013.01.008  0.36
2013 Soth M, Hermann JC, Yee C, Alam M, Barnett JW, Berry P, Browner MF, Frank K, Frauchiger S, Harris S, He Y, Hekmat-Nejad M, Hendricks T, Henningsen R, Hilgenkamp R, ... ... Shaw D, et al. 3-Amido pyrrolopyrazine JAK kinase inhibitors: development of a JAK3 vs JAK1 selective inhibitor and evaluation in cellular and in vivo models. Journal of Medicinal Chemistry. 56: 345-56. PMID 23214979 DOI: 10.1021/jm301646k  0.36
2013 Schmidt AG, Xu H, Khan AR, O'Donnell T, Khurana S, King LR, Manischewitz J, Golding H, Suphaphiphat P, Carfi A, Settembre EC, Dormitzer PR, Kepler TB, Zhang R, Moody MA, ... ... Shaw DE, et al. 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. 110: 264-9. PMID 23175789 DOI: 10.1073/pnas.1218256109  0.36
2013 Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE. Correction: Systematic validation of protein force fields against experimental data (PLoS ONE) Plos One. 8. DOI: 10.1371/annotation/8301b5d4-1ba3-40e7-8fcd-3e169b967044  0.36
2013 Grossman JP, Towles B, Bank JA, Shaw DE. The role of cascade, a cycle-based simulation infrastructure, in designing the anton special-purpose supercomputers Proceedings - Design Automation Conference. DOI: 10.1145/2463209.2488884  0.36
2013 Grossman JP, Kuskin JS, Bank JA, Theobald M, Dror RO, Ierardi DJ, Larson RH, Ben Schafer U, Towles B, Young C, Shaw DE. Hardware support for fine-grained event-driven computation in anton 2 International Conference On Architectural Support For Programming Languages and Operating Systems - Asplos. 549-560. DOI: 10.1145/2451116.2451175  0.36
2013 Scarpazza DP, Ierardi DJ, Lerer AK, Mackenzie KM, Pan AC, Bank JA, Chow E, Dror RO, Grossman JP, Killebrew D, Moraes MA, Predescu C, Salmon JK, Shaw DE. Extending the generality of molecular dynamics simulations on a special-purpose machine Proceedings - Ieee 27th International Parallel and Distributed Processing Symposium, Ipdps 2013. 933-945. DOI: 10.1109/IPDPS.2013.93  0.36
2012 Dirks RM, Xu H, Shaw DE. Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations. Journal of Chemical Theory and Computation. 8: 162-71. PMID 26592879 DOI: 10.1021/ct200464v  0.32
2012 Zhang C, Srinivasan Y, Arlow DH, Fung JJ, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE, Weis WI, Coughlin SR, Kobilka BK. High-resolution crystal structure of human protease-activated receptor 1. Nature. 492: 387-92. PMID 23222541 DOI: 10.1038/nature11701  0.36
2012 Piana S, Lindorff-Larsen K, Shaw DE. Protein folding kinetics and thermodynamics from atomistic simulation. Proceedings of the National Academy of Sciences of the United States of America. 109: 17845-50. PMID 22822217 DOI: 10.1073/pnas.1201811109  0.36
2012 Bandaranayake RM, Ungureanu D, Shan Y, Shaw DE, Silvennoinen O, Hubbard SR. Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F. Nature Structural & Molecular Biology. 19: 754-9. PMID 22820988 DOI: 10.1038/nsmb.2348  0.36
2012 Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE. Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. Plos One. 7: e39918. PMID 22768169 DOI: 10.1371/journal.pone.0039918  0.36
2012 Yang MH, Nickerson S, Kim ET, Liot C, Laurent G, Spang R, Philips MR, Shan Y, Shaw DE, Bar-Sagi D, Haigis MC, Haigis KM. Regulation of RAS oncogenicity by acetylation. Proceedings of the National Academy of Sciences of the United States of America. 109: 10843-8. PMID 22711838 DOI: 10.1073/pnas.1201487109  0.36
2012 Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, Dror RO, Jumper J, Kuriyan J, Shaw DE. Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell. 149: 860-70. PMID 22579287 DOI: 10.1016/j.cell.2012.02.063  0.36
2012 Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. Biomolecular simulation: a computational microscope for molecular biology. Annual Review of Biophysics. 41: 429-52. PMID 22577825 DOI: 10.1146/annurev-biophys-042910-155245  0.36
2012 Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins. 80: 2071-9. PMID 22513870 DOI: 10.1002/prot.24098  0.36
2012 Jensen MØ, Jogini V, Borhani DW, Leffler AE, Dror RO, Shaw DE. Mechanism of voltage gating in potassium channels. Science (New York, N.Y.). 336: 229-33. PMID 22499946 DOI: 10.1126/science.1216533  0.36
2012 Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE. Systematic validation of protein force fields against experimental data. Plos One. 7: e32131. PMID 22384157 DOI: 10.1371/journal.pone.0032131  0.36
2012 Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PS, Dror RO, Shaw DE, Weis WI, Wess J, Kobilka BK. Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature. 482: 552-6. PMID 22358844 DOI: 10.1038/nature10867  0.36
2012 Lindorff-Larsen K, Trbovic N, Maragakis P, Piana S, Shaw DE. Structure and dynamics of an unfolded protein examined by molecular dynamics simulation Journal of the American Chemical Society. 134: 3787-3791. PMID 22339051 DOI: 10.1021/ja209931w  0.36
2012 Borhani DW, Shaw DE. The future of molecular dynamics simulations in drug discovery Journal of Computer-Aided Molecular Design. 26: 15-26. PMID 22183577 DOI: 10.1007/s10822-011-9517-y  0.36
2012 Predescu C, Lippert RA, Eastwood MP, Ierardi D, Xu H, Jensen M, Bowers KJ, Gullingsrud J, Rendleman CA, Dror RO, Shaw DE. Computationally efficient molecular dynamics integrators with improved sampling accuracy Molecular Physics. 110: 967-983. DOI: 10.1080/00268976.2012.681311  0.36
2012 Dirks RM, Xu H, Shaw DE. Improving sampling by exchanging hamiltonians with efficiently configured nonequilibrium simulations Journal of Chemical Theory and Computation. 8: 162-171. DOI: 10.1021/ct200464v  0.36
2012 Chow E, Klepeis JL, Rendleman CA, Dror RO, Shaw DE. New technologies for molecular dynamics simulations Comprehensive Biophysics. 9: 86-104. DOI: 10.1016/B978-0-12-374920-8.00908-5  0.36
2011 Lindorff-Larsen K, Piana S, Dror RO, Shaw DE. How fast-folding proteins fold. Science (New York, N.Y.). 334: 517-20. PMID 22034434 DOI: 10.1126/science.1208351  0.36
2011 Dror RO, Arlow DH, Maragakis P, Mildorf TJ, Pan AC, Xu H, Borhani DW, Shaw DE. Activation mechanism of the β2-adrenergic receptor. Proceedings of the National Academy of Sciences of the United States of America. 108: 18684-9. PMID 22031696 DOI: 10.1073/pnas.1110499108  0.36
2011 Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y, Xu H, Shaw DE. 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: 13118-23. PMID 21778406 DOI: 10.1073/pnas.1104614108  0.36
2011 Shan Y, Kim ET, Eastwood MP, Dror RO, Seeliger MA, Shaw DE. How does a drug molecule find its target binding site? Journal of the American Chemical Society. 133: 9181-3. PMID 21545110 DOI: 10.1021/ja202726y  0.36
2011 Piana S, Lindorff-Larsen K, Shaw DE. How robust are protein folding simulations with respect to force field parameterization? Biophysical Journal. 100: L47-L49. PMID 21539772 DOI: 10.1016/j.bpj.2011.03.051  0.36
2011 Kuglstatter A, Wong A, Tsing S, Lee SW, Lou Y, Villaseñor AG, Bradshaw JM, Shaw D, Barnett JW, Browner MF. Insights into the conformational flexibility of Bruton's tyrosine kinase from multiple ligand complex structures. Protein Science : a Publication of the Protein Society. 20: 428-36. PMID 21280133 DOI: 10.1002/pro.575  0.36
2011 Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SG, Choi HJ, Devree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, et al. Structure and function of an irreversible agonist-β(2) adrenoceptor complex. Nature. 469: 236-40. PMID 21228876 DOI: 10.1038/nature09665  0.36
2011 Kenny HA, Leonhardt P, Ladanyi A, Yamada SD, Montag A, Im HK, Jagadeeswaran S, Shaw DE, Mazar AP, Lengyel E. Targeting the urokinase plasminogen activator receptor inhibits ovarian cancer metastasis Clinical Cancer Research. 17: 459-471. PMID 21149615 DOI: 10.1158/1078-0432.CCR-10-2258  0.36
2011 Piana S, Sarkar K, Lindorff-Larsen K, Guo M, Gruebele M, Shaw DE. Computational design and experimental testing of the fastest-folding β-sheet protein. Journal of Molecular Biology. 405: 43-8. PMID 20974152 DOI: 10.1016/j.jmb.2010.10.023  0.36
2011 Salmon JK, Moraes MA, Dror RO, Shaw DE. Parallel random numbers: As easy as 1, 2, 3 Proceedings of 2011 Sc - International Conference For High Performance Computing, Networking, Storage and Analysis. DOI: 10.1145/2063384.2063405  0.36
2011 Dror RO, Grossman JP, MacKenzie KM, Towles B, Chow E, Salmon JK, Young C, Bank JA, Batson B, Deneroff MM, Kuskin JS, Larson RH, Moraes MA, Shaw DE. Overcoming communication latency barriers in massively parallel scientific computation Ieee Micro. 31: 8-19. DOI: 10.1109/MM.2011.38  0.36
2011 Tang PTP, Butts JA, Dror RO, Shaw DE. Tight certification techniques for digit-by-rounding algorithms with application to a new 1/√x design Proceedings - Symposium On Computer Arithmetic. 159-168. DOI: 10.1109/ARITH.2011.29  0.36
2011 Butts JA, Tang PTP, Dror RO, Shaw DE. Radix-8 digit-by-rounding: Achieving high-performance reciprocals, square roots, and reciprocal square roots Proceedings - Symposium On Computer Arithmetic. 149-158. DOI: 10.1109/ARITH.2011.28  0.36
2010 Eastwood MP, Stafford KA, Lippert RA, Jensen MØ, Maragakis P, Predescu C, Dror RO, Shaw DE. Equipartition and the Calculation of Temperature in Biomolecular Simulations. Journal of Chemical Theory and Computation. 6: 2045-58. PMID 26615934 DOI: 10.1021/ct9002916  0.36
2010 Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-level characterization of the structural dynamics of proteins. Science (New York, N.Y.). 330: 341-6. PMID 20947758 DOI: 10.1126/science.1187409  0.36
2010 Rabbani SA, Ateeq B, Arakelian A, Valentino ML, Shaw DE, Dauffenbach LM, Kerfoot CA, Mazar AP. An anti-urokinase plasminogen activator receptor antibody (ATN-658) blocks prostate cancer invasion, migration, growth, and experimental skeletal metastasis in vitro and in vivo Neoplasia. 12: 778-788. PMID 20927316 DOI: 10.1593/neo.10296  0.36
2010 Kuglstatter A, Ghate M, Tsing S, Villaseñor AG, Shaw D, Barnett JW, Browner MF. X-ray crystal structure of JNK2 complexed with the p38α inhibitor BIRB796: Insights into the rational design of DFG-out binding MAP kinase inhibitors Bioorganic and Medicinal Chemistry Letters. 20: 5217-5220. PMID 20655210 DOI: 10.1016/j.bmcl.2010.06.157  0.36
2010 Kutach AK, Villaseñor AG, Lam D, Belunis C, Janson C, Lok S, Hong LN, Liu CM, Deval J, Novak TJ, Barnett JW, Chu W, Shaw D, Kuglstatter A. Crystal structures of IL-2-inducible T cell kinase complexed with inhibitors: insights into rational drug design and activity regulation. Chemical Biology & Drug Design. 76: 154-63. PMID 20545945 DOI: 10.1111/j.1747-0285.2010.00993.x  0.36
2010 Dror RO, Jensen MØ, Borhani DW, Shaw DE. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. The Journal of General Physiology. 135: 555-62. PMID 20513757 DOI: 10.1085/jgp.200910373  0.36
2010 Latour DR, Jekle A, Javanbakht H, Henningsen R, Gee P, Lee I, Tran P, Ren S, Kutach AK, Harris SF, Wang SM, Lok SJ, Shaw D, Li J, Heilek G, et al. Biochemical characterization of the inhibition of the dengue virus RNA polymerase by beta-d-2'-ethynyl-7-deaza-adenosine triphosphate. Antiviral Research. 87: 213-22. PMID 20470829 DOI: 10.1016/j.antiviral.2010.05.003  0.36
2010 Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 78: 1950-8. PMID 20408171 DOI: 10.1002/prot.22711  0.36
2010 Jensen MØ, Borhani DW, Lindorff-Larsen K, Maragakis P, Jogini V, Eastwood MP, Dror RO, Shaw DE. Principles of conduction and hydrophobic gating in K+ channels. Proceedings of the National Academy of Sciences of the United States of America. 107: 5833-8. PMID 20231479 DOI: 10.1073/pnas.0911691107  0.36
2010 Bowers KJ, Lippert RA, Dror RO, Shaw DE. Improved twiddle access for fast Fourier transforms Ieee Transactions On Signal Processing. 58: 1122-1130. DOI: 10.1109/TSP.2009.2035984  0.36
2010 Dror RO, Grossman JP, Mackenzie KM, Towles B, Chow E, Salmon JK, Young C, Bank JA, Batson B, Deneroff MM, Kuskin JS, Larson RH, Moraes MA, Shaw DE. Exploiting 162-nanosecond end-to-end communication latency on Anton 2010 Acm/Ieee International Conference For High Performance Computing, Networking, Storage and Analysis, Sc 2010. DOI: 10.1109/SC.2010.23  0.36
2010 Jensen M, Borhani DW, Lindorff-Larsen K, Dror RO, Shaw DE. Reply to Domene and Furini: Distinguishing knock-on and vacancy diffusion mechanisms Proceedings of the National Academy of Sciences of the United States of America. 107: E129. DOI: 10.1073/pnas.1008197107  0.36
2010 Eastwood MP, Stafford KA, Lippert RA, Jensen M, Maragakis P, Predescu C, Dror RO, Shaw DE. Equipartition and the calculation of temperature in biomolecular simulations Journal of Chemical Theory and Computation. 6: 2045-2058. DOI: 10.1021/ct9002916  0.36
2009 Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 5: 2595-605. PMID 26631775 DOI: 10.1021/ct900229u  0.6
2009 Jura N, Shan Y, Cao X, Shaw DE, Kuriyan J. 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. 106: 21608-21613. PMID 20007378 DOI: 10.1073/pnas.0912101106  0.36
2009 Dror RO, Jensen MØ, Shaw DE. Elucidating membrane protein function through long-timescale molecular dynamics simulation. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 2340-2. PMID 19965181 DOI: 10.1109/IEMBS.2009.5335057  0.36
2009 Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE. Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 046705. PMID 19905480  0.36
2009 Kwan J, Ling A, Papp E, Shaw D, Bradshaw JM. A fluorescence resonance energy transfer-based binding assay for characterizing kinase inhibitors: important role for C-terminal biotin tagging of the kinase. Analytical Biochemistry. 395: 256-62. PMID 19716360 DOI: 10.1016/j.ab.2009.08.032  0.36
2009 Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology. 19: 120-7. PMID 19361980 DOI: 10.1016/j.sbi.2009.03.004  0.36
2009 Seeliger MA, Ranjitkar P, Kasap C, Shan Y, Shaw DE, Shah NP, Kuriyan J, Maly DJ. Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations Cancer Research. 69: 2384-2392. PMID 19276351 DOI: 10.1158/0008-5472.CAN-08-3953  0.36
2009 Dror RO, Arlow DH, Borhani DW, Jensen MØ, Piana S, Shaw DE. Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proceedings of the National Academy of Sciences of the United States of America. 106: 4689-94. PMID 19258456 DOI: 10.1073/pnas.0811065106  0.36
2009 Villaseñor AG, Kondru R, Ho H, Wang S, Papp E, Shaw D, Barnett JW, Browner MF, Kuglstatter A. Structural insights for design of potent spleen tyrosine kinase inhibitors from crystallographic analysis of three inhibitor complexes. Chemical Biology & Drug Design. 73: 466-70. PMID 19220318 DOI: 10.1111/j.1747-0285.2009.00785.x  0.36
2009 Shan Y, Seeliger MA, Eastwood MP, Frank F, Xu H, Jensen MØ, Dror RO, Kuriyan J, Shaw DE. 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: 139-44. PMID 19109437 DOI: 10.1073/pnas.0811223106  0.36
2009 Shaw DE, Dror RO, Salmon JK, Grossman JP, MacKenzie KM, Bank JA, Young C, Deneroff MM, Batson B, Bowers KJ, Chow E, Eastwood MP, Ierardi DJ, Klepeis JL, Kuskin JS, et al. Millisecond-scale molecular dynamics simulations on Anton Proceedings of the Conference On High Performance Computing Networking, Storage and Analysis, Sc '09. DOI: 10.1145/1654059.1654099  0.36
2009 Young C, Bank JA, Dror RO, Grossman JP, Salmon JK, Shaw DE. A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton Proceedings of the Conference On High Performance Computing Networking, Storage and Analysis, Sc '09. DOI: 10.1145/1654059.1654083  0.36
2009 Shenfeld DK, Xu H, Eastwood MP, Dror RO, Shaw DE. Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 80. DOI: 10.1103/PhysRevE.80.046705  0.36
2009 Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. Automated event detection and activity monitoring in long molecular dynamics simulations Journal of Chemical Theory and Computation. 5: 2595-2605. DOI: 10.1021/ct900229u  0.36
2008 Jensen MØ, Dror RO, Xu H, Borhani DW, Arkin IT, Eastwood MP, Shaw DE. 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: 14430-5. PMID 18787121 DOI: 10.1073/pnas.0802401105  0.36
2008 Juarez JC, Manuia M, Burnett ME, Betancourt O, Boivin B, Shaw DE, Tonks NK, Mazar AP, Doñate F. Superoxide dismutase 1 (SOD1) is essential for H2O2-mediated oxidation and inactivation of phosphatases in growth factor signaling. Proceedings of the National Academy of Sciences of the United States of America. 105: 7147-52. PMID 18480265 DOI: 10.1073/pnas.0709451105  0.36
2008 Doñate F, Parry GC, Shaked Y, Hensley H, Guan X, Beck I, Tel-Tsur Z, Plunkett ML, Manuia M, Shaw DE, Kerbel RS, Mazar AP. Pharmacology of the novel antiangiogenic peptide ATN-161 (Ac-PHSCN-NH2): observation of a U-shaped dose-response curve in several preclinical models of angiogenesis and tumor growth. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 14: 2137-44. PMID 18381955 DOI: 10.1158/1078-0432.CCR-07-4530  0.36
2008 Huai Q, Zhou A, Lin L, Mazar AP, Parry GC, Callahan J, Shaw DE, Furie B, Furie BC, Huang M. Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes. Nature Structural & Molecular Biology. 15: 422-3. PMID 18376415 DOI: 10.1038/nsmb.1404  0.36
2008 Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Iii AG, Shaw DE. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8. PMID 18311962 DOI: 10.1021/jp077018h  0.36
2008 Doñate F, Juarez JC, Burnett ME, Manuia MM, Guan X, Shaw DE, Smith EL, Timucin C, Braunstein MJ, Batuman OA, Mazar AP. Identification of biomarkers for the antiangiogenic and antitumour activity of the superoxide dismutase 1 (SOD1) inhibitor tetrathiomolybdate (ATN-224). British Journal of Cancer. 98: 776-83. PMID 18253124 DOI: 10.1038/sj.bjc.6604226  0.36
2008 Grossman JP, Young C, Bank JA, Mackenzie K, Lerardi DJ, Salmon JK, Dror RO, Shaw DE. Simulation and embedded software development for anton, a parallel machine with heterogeneous multicore ASICs Embedded Systems Week 2008 - Proceedings of the 6th Ieee/Acm/Ifip International Conference On Hardware/Software Codesign and System Synthesis, Codes+Isss 2008. 125-130. DOI: 10.1145/1450135.1450165  0.36
2008 Shaw DE, Deneroff MM, Dror RO, Kuskin JS, Larson RH, Salmon JK, Young C, Batson B, Bowers KJ, Chao JC, Eastwood MP, Gagliardo J, Grossman JP, Ho CR, Lerardi DJ, et al. Anton, a special-purpose machine for molecular dynamics simulation Communications of the Acm. 51: 91-97. DOI: 10.1145/1364782.1364802  0.36
2008 Tu T, Rendleman CA, Borhani DW, Dror RO, Gullingsrud J, Jensen MO, Klepeis JL, Maragakis P, Miller P, Stafford KA, Shaw DE. A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories 2008 Sc - International Conference For High Performance Computing, Networking, Storage and Analysis, Sc 2008. DOI: 10.1109/SC.2008.5214715  0.36
2008 Shaw DE. Architectures and algorithms for millisecond-scale molecular dynamics simulations of proteins Proceedings of the Annual International Symposium On Microarchitecture, Micro. ii. DOI: 10.1109/MICRO.2008.4771773  0.36
2008 Grossman JP, Salmon JK, Ho CR, Ierardi DJ, Towles B, Batson B, Spengler J, Wang SC, Mueller R, Theobald M, Young C, Gagliardo J, Deneroff MM, Dror RO, Shaw DE. Hierarchical simulation-based verification of anton, a special-purpose parallel machine 26th Ieee International Conference On Computer Design 2008, Iccd. 340-347. DOI: 10.1109/ICCD.2008.4751883  0.36
2008 Kuskin JS, Young C, Grossman JP, Batson B, Deneroff MM, Dror RO, Shaw DE. Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation Proceedings - International Symposium On High-Performance Computer Architecture. 343-354. DOI: 10.1109/HPCA.2008.4658651  0.36
2008 Larson RH, Salmon JK, Dror RO, Deneroff MM, Young C, Grossman JP, Shan Y, Klepeis JL, Shaw DE. High-throughput pairwise point interactions in anton, a specialized machine for molecular dynamics simulation Proceedings - International Symposium On High-Performance Computer Architecture. 331-342. DOI: 10.1109/HPCA.2008.4658650  0.36
2008 Ho CR, Theobald M, Deneroff MM, Dror RO, Gagliardo J, Shaw DE. Early formal verification of conditional coverage points to identify intrinsically hard-to-verify logic Proceedings - Design Automation Conference. 268-271. DOI: 10.1109/DAC.2008.4555821  0.36
2007 Arkin IT, Xu H, Jensen MØ, Arbely E, Bennett ER, Bowers KJ, Chow E, Dror RO, Eastwood MP, Flitman-Tene R, Gregersen BA, Klepeis JL, Kolossváry I, Shan Y, Shaw DE. Mechanism of Na+/H+ antiporting. Science (New York, N.Y.). 317: 799-803. PMID 17690293 DOI: 10.1126/science.1142824  0.36
2007 Lippert RA, Bowers KJ, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Shaw DE. A common, avoidable source of error in molecular dynamics integrators. The Journal of Chemical Physics. 126: 046101. PMID 17286520 DOI: 10.1063/1.2431176  0.36
2007 Danese S, Sans M, Spencer DM, Beck I, Doñate F, Plunkett ML, de la Motte C, Redline R, Shaw DE, Levine AD, Mazar AP, Fiocchi C. Angiogenesis blockade as a new therapeutic approach to experimental colitis. Gut. 56: 855-62. PMID 17170016 DOI: 10.1136/gut.2006.114314  0.36
2007 Li Y, Parry G, Chen L, Callahan JA, Shaw DE, Meehan EJ, Mazar AP, Huang M. An anti-urokinase plasminogen activator receptor (uPAR) antibody: crystal structure and binding epitope. Journal of Molecular Biology. 365: 1117-29. PMID 17101149 DOI: 10.1016/j.jmb.2006.10.059  0.36
2007 Bowers KJ, Dror RO, Shaw DE. Zonal methods for the parallel execution of range-limited N-body simulations Journal of Computational Physics. 221: 303-329. DOI: 10.1016/j.jcp.2006.06.014  0.36
2006 Allan AL, Gladstone PL, Price ML, Hopkins SA, Juarez JC, Doñate F, Ternansky RJ, Shaw DE, Ganem B, Li Y, Wang W, Ealick S. Synthesis and evaluation of multisubstrate bicyclic pyrimidine nucleoside inhibitors of human thymidine phosphorylase. Journal of Medicinal Chemistry. 49: 7807-15. PMID 17181163 DOI: 10.1021/jm060428u  0.36
2006 Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design. 20: 647-71. PMID 17124629 DOI: 10.1007/s10822-006-9087-6  0.36
2006 Khalili P, Arakelian A, Chen G, Plunkett ML, Beck I, Parry GC, Doñate F, Shaw DE, Mazar AP, Rabbani SA. A non-RGD-based integrin binding peptide (ATN-161) blocks breast cancer growth and metastasis in vivo. Molecular Cancer Therapeutics. 5: 2271-80. PMID 16985061 DOI: 10.1158/1535-7163.MCT-06-0100  0.36
2006 Barinka C, Parry G, Callahan J, Shaw DE, Kuo A, Bdeir K, Cines DB, Mazar A, Lubkowski J. Structural basis of interaction between urokinase-type plasminogen activator and its receptor. Journal of Molecular Biology. 363: 482-95. PMID 16979660 DOI: 10.1016/j.jmb.2006.08.063  0.36
2006 Juarez JC, Betancourt O, Pirie-Shepherd SR, Guan X, Price ML, Shaw DE, Mazar AP, Doñate F. Copper binding by tetrathiomolybdate attenuates angiogenesis and tumor cell proliferation through the inhibition of superoxide dismutase 1. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 12: 4974-82. PMID 16914587 DOI: 10.1158/1078-0432.CCR-06-0171  0.36
2006 Bowers KJ, Dror RO, Shaw DE. The midpoint method for parallelization of particle simulations. The Journal of Chemical Physics. 124: 184109. PMID 16709099 DOI: 10.1063/1.2191489  0.36
2006 Cianfrocca ME, Kimmel KA, Gallo J, Cardoso T, Brown MM, Hudes G, Lewis N, Weiner L, Lam GN, Brown SC, Shaw DE, Mazar AP, Cohen RB. Phase 1 trial of the antiangiogenic peptide ATN-161 (Ac-PHSCN-NH(2)), a beta integrin antagonist, in patients with solid tumours. British Journal of Cancer. 94: 1621-6. PMID 16705310 DOI: 10.1038/sj.bjc.6603171  0.36
2006 Huai Q, Mazar AP, Kuo A, Parry GC, Shaw DE, Callahan J, Li Y, Yuan C, Bian C, Chen L, Furie B, Furie BC, Cines DB, Huang M. Structure of human urokinase plasminogen activator in complex with its receptor. Science (New York, N.Y.). 311: 656-9. PMID 16456079 DOI: 10.1126/science.1121143  0.36
2006 Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE. Scalable algorithms for molecular dynamics simulations on commodity clusters Proceedings of the 2006 Acm/Ieee Conference On Supercomputing, Sc'06. DOI: 10.1145/1188455.1188544  0.36
2006 Shaw DE. New architectures for a new biology Proceedings - International Symposium On High-Performance Computer Architecture. 2006: 1. DOI: 10.1109/HPCA.2006.1598107  0.36
2005 McCrae KR, Doñate F, Merkulov S, Sun D, Qi X, Shaw DE. Inhibition of angiogenesis by cleaved high molecular weight kininogen (HKa) and HKa domain 5. Current Cancer Drug Targets. 5: 519-28. PMID 16305348 DOI: 10.2174/156800905774574039  0.36
2005 Shaw DE. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. Journal of Computational Chemistry. 26: 1318-28. PMID 16013057 DOI: 10.1002/jcc.20267  0.36
2005 Shan Y, Klepeis JL, Eastwood MP, Dror RO, Shaw DE. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. The Journal of Chemical Physics. 122: 54101. PMID 15740304 DOI: 10.1063/1.1839571  0.36
2005 Bowers KJ, Dror RO, Shaw DE. Overview of neutral territory methods for the parallel evaluation of pairwise particle interactions Journal of Physics: Conference Series. 16: 300-304. DOI: 10.1088/1742-6596/16/1/041  0.36
2004 Doñate F, McCrae K, Shaw DE, Mazar AP. Extracellular tropomyosin: a novel common pathway target for anti-angiogenic therapy. Current Cancer Drug Targets. 4: 543-53. PMID 15578912 DOI: 10.2174/1568009043332781  0.36
2004 Doñate F, Juarez JC, Guan X, Shipulina NV, Plunkett ML, Tel-Tsur Z, Shaw DE, Morgan WT, Mazar AP. Peptides derived from the histidine-proline domain of the histidine-proline-rich glycoprotein bind to tropomyosin and have antiangiogenic and antitumor activities. Cancer Research. 64: 5812-7. PMID 15313924 DOI: 10.1158/0008-5472.CAN-04-0440  0.36
2004 Guan X, Juarez JC, Qi X, Shipulina NV, Shaw DE, Morgan WT, McCrae KR, Mazar AP, Doñate F. Histidine-proline rich glycoprotein (HPRG) binds and transduces anti-angiogenic signals through cell surface tropomyosin on endothelial cells. Thrombosis and Haemostasis. 92: 403-12. PMID 15269838 DOI: 10.1267/THRO04080403  0.36
2004 Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 55: 351-67. PMID 15048827 DOI: 10.1002/prot.10613  0.36
2004 Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry. 47: 1739-49. PMID 15027865 DOI: 10.1021/jm0306430  0.36
2002 Juarez JC, Guan X, Shipulina NV, Plunkett ML, Parry GC, Shaw DE, Zhang JC, Rabbani SA, McCrae KR, Mazar AP, Morgan WT, Doñate F. Histidine-proline-rich glycoprotein has potent antiangiogenic activity mediated through the histidine-proline-rich domain. Cancer Research. 62: 5344-50. PMID 12235005  0.36
2000 Zhang JC, Claffey K, Sakthivel R, Darzynkiewicz Z, Shaw DE, Leal J, Wang YC, Lu FM, McCrae KR. Two-chain high molecular weight kininogen induces endothelial cell apoptosis and inhibits angiogenesis: partial activity within domain 5. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 14: 2589-600. PMID 11099478 DOI: 10.1096/fj.99-1025com  0.36
2000 El Yazal J, Prendergast FG, Shaw DE, Pang YP. Protonation states of the chromophore of denatured green fluorescent proteins predicted by ab initio calculations Journal of the American Chemical Society. 122: 11411-11415. DOI: 10.1021/ja0008721  0.36
2000 Zhang J, Juarez J, Shaw DE, Mazar AP, McCrae KR. Pefitdes derived from high molecular weight kininogen (hk) domains 3 and 5 inhibit endothelial cell proliferation and induce endothelial cell apoptosis Blood. 96: 41a.  0.36
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