| Year |
Citation |
Score |
| 2023 |
Ayaz P, Lyczek A, Paung Y, Mingione VR, Iacob RE, de Waal PW, Engen JR, Seeliger MA, Shan Y, Shaw DE. Structural mechanism of a drug-binding process involving a large conformational change of the protein target. Nature Communications. 14: 1885. PMID 37019905 DOI: 10.1038/s41467-023-36956-5 |
0.608 |
|
| 2022 |
Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. 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. 126: 4442-4457. PMID 35694853 DOI: 10.1021/acs.jpcb.1c10971 |
0.451 |
|
| 2022 |
Shan Y, Mysore VP, Leffler AE, Kim ET, Sagawa S, Shaw DE. How does a small molecule bind at a cryptic binding site? Plos Computational Biology. 18: e1009817. PMID 35239648 DOI: 10.1371/journal.pcbi.1009817 |
0.53 |
|
| 2022 |
Campbell MR, Ruiz-Saenz A, Peterson E, Agnew C, Ayaz P, Garfinkle S, Littlefield P, Steri V, Oeffinger J, Sampang M, Shan Y, Shaw DE, Jura N, Moasser MM. Targetable HER3 functions driving tumorigenic signaling in HER2-amplified cancers. Cell Reports. 38: 110291. PMID 35108525 DOI: 10.1016/j.celrep.2021.110291 |
0.565 |
|
| 2021 |
Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, ... Shaw DE, et al. A structural model of a Ras-Raf signalosome. Nature Structural & Molecular Biology. 28: 847-857. PMID 34625747 DOI: 10.1038/s41594-021-00667-6 |
0.511 |
|
| 2021 |
Agnew C, Ayaz P, Kashima R, Loving HS, Ghatpande P, Kung JE, Underbakke ES, Shan Y, Shaw DE, Hata A, Jura N. Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization. Nature Communications. 12: 4950. PMID 34400635 DOI: 10.1038/s41467-021-25248-5 |
0.565 |
|
| 2020 |
Yan XE, Ayaz P, Zhu SJ, Zhao P, Liang L, Zhang CH, Wu YC, Li JL, Choi HG, Huang X, Shan Y, Shaw DE, Yun CH. Structural basis of AZD9291 selectivity for EGFR T790M. Journal of Medicinal Chemistry. PMID 32672461 DOI: 10.1021/Acs.Jmedchem.0C00891 |
0.629 |
|
| 2020 |
Jiang S, Feher M, Williams CI, Cole B, Shaw DE. AutoPH4: An automated method for generating pharmacophore models from protein binding pockets. Journal of Chemical Information and Modeling. PMID 32639159 DOI: 10.1021/Acs.Jcim.0C00121 |
0.318 |
|
| 2020 |
Robustelli P, Piana S, Shaw DE. The mechanism of coupled folding-upon-binding of an intrinsically disordered protein. Journal of the American Chemical Society. PMID 32323533 DOI: 10.1021/Jacs.0C03217 |
0.387 |
|
| 2020 |
Piana S, Robustelli P, Tan D, Chen S, Shaw DE. Development of a force field for the simulation of single-chain proteins and protein-protein complexes. Journal of Chemical Theory and Computation. PMID 31914313 DOI: 10.1021/Acs.Jctc.9B00251 |
0.526 |
|
| 2019 |
Giordanetto F, Jin C, Willmore L, Feher M, Shaw DE. Fragment hits: What do they look like and how do they bind? Journal of Medicinal Chemistry. PMID 30875465 DOI: 10.1021/Acs.Jmedchem.8B01855 |
0.329 |
|
| 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 |
0.344 |
|
| 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 |
0.612 |
|
| 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 |
0.341 |
|
| 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 |
0.354 |
|
| 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 |
0.38 |
|
| 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 |
0.328 |
|
| 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 |
0.512 |
|
| 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 |
0.349 |
|
| 2017 |
Robustelli P, Piana S, Shaw DE. Developing Force Fields for the Accurate Simulation of Both Ordered and Disordered Protein States Biophysical Journal. 112: 175a. DOI: 10.1016/J.Bpj.2016.11.970 |
0.337 |
|
| 2017 |
Koldsø H, Jensen MØ, Jogini V, Shaw DE. Permeation, Gating, and Modulation of the TRPA1 Channel in Long-Timescale Molecular Dynamics Simulations Biophysical Journal. 112: 466a. DOI: 10.1016/J.Bpj.2016.11.2497 |
0.322 |
|
| 2017 |
Needham SR, Zanetti-Domigues LC, Arkhipov A, Mysore VP, Korovesis D, Roberts SK, Tynan CJ, Rolfe DJ, Hirsch M, Lajevardipour A, Clayton AH, Parker PJ, Shan Y, Shaw DE, Martin-Fernandez ML. Oligomerization of the Epidermal Growth Factor Receptor Organizes Kinase-Active Dimers into Competent Signaling Platforms Biophysical Journal. 112: 26a-27a. DOI: 10.1016/J.Bpj.2016.11.180 |
0.578 |
|
| 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 |
0.624 |
|
| 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 |
0.365 |
|
| 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 |
0.6 |
|
| 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 |
0.391 |
|
| 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 |
0.353 |
|
| 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 |
0.306 |
|
| 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 |
0.335 |
|
| 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 |
0.609 |
|
| 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 |
0.334 |
|
| 2015 |
Pan AC, Weinreich TM, Piana S, Shaw DE. Using Long-Timescale Molecular Dynamics Simulations to Benchmark Enhanced Sampling Methods Biophysical Journal. 108: 183a. DOI: 10.1016/J.Bpj.2014.11.1014 |
0.355 |
|
| 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 |
0.565 |
|
| 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 |
0.625 |
|
| 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 |
0.585 |
|
| 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 |
0.622 |
|
| 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 |
0.573 |
|
| 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 |
0.583 |
|
| 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 |
0.372 |
|
| 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. Author response: How IGF-1 activates its receptor Elife. DOI: 10.7554/Elife.03772.036 |
0.536 |
|
| 2014 |
Shan Y, Kim E, Eastwood MP, Dror RO, Seeliger MA, Shaw DE. Correction to How Does a Drug Molecule Find its Target Binding Site? Journal of the American Chemical Society. 136: 3320-3320. DOI: 10.1021/Ja500545U |
0.53 |
|
| 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 |
0.503 |
|
| 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 |
0.378 |
|
| 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 |
0.377 |
|
| 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 |
0.62 |
|
| 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 |
0.338 |
|
| 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 |
0.648 |
|
| 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 |
0.357 |
|
| 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 |
0.624 |
|
| 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 |
0.578 |
|
| 2013 |
Arkhipov A, Shan Y, Kim ET, Dror RO, Shaw DE. Author response: Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family Elife. DOI: 10.7554/Elife.00708.011 |
0.551 |
|
| 2013 |
Endres N, Das R, Smith A, Arkhipov A, Kovacs E, Huang Y, Pelton J, Shan Y, Shaw D, Wemmer D, Groves J, Kuriyan J. EGFR transmembrane - juxtamembrane (TM-JM) segment in bicelles: MD guided NMR refined structure. Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2M20/Pdb |
0.562 |
|
| 2013 |
Shaw DE. Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Biophysical Journal. 104: 45a. DOI: 10.1016/J.Bpj.2012.11.289 |
0.374 |
|
| 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 |
0.358 |
|
| 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 |
0.614 |
|
| 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 |
0.361 |
|
| 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 |
0.535 |
|
| 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 |
0.616 |
|
| 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 |
0.38 |
|
| 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 |
0.381 |
|
| 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: 10.1016/J.Bpj.2011.11.2241 |
0.534 |
|
| 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 |
0.567 |
|
| 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 |
0.321 |
|
| 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 |
|
| 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 |
0.566 |
|
| 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 |
0.328 |
|
| 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 |
0.559 |
|
| 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 |
0.618 |
|
| 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 |
0.595 |
|
| 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: 10.1016/J.Bpj.2008.12.1964 |
0.347 |
|
| 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 |
0.626 |
|
| 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 |
0.516 |
|
| 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 |
0.523 |
|
| 2009 |
Piana-Agostinetti S, Lindorff-Larsen K, Maragakis P, Eastwood MP, Dror RO, Shaw DE. Improving Molecular Mechanics Force Fields By Comparison Of Microsecond Simulations With Nmr Experiments Biophysical Journal. 96: 406a. DOI: 10.1016/J.Bpj.2008.12.2066 |
0.367 |
|
| 2009 |
Wriggers W, Stafford KA, Shan Y, Piana-Agostinetti S, Maragakis P, Lindorff-Larsen K, Miller PJ, Eastwood MP, Dror RO, Shaw DE. Automated Event Detection and Activity Monitoring in Long Time-Scale Molecular Dynamics Biophysical Journal. 96: 364a-365a. DOI: 10.1016/J.Bpj.2008.12.1962 |
0.592 |
|
| 2008 |
Tsang E, Giannetti AM, Shaw D, Dinh M, Tse JK, Gandhi S, Ho H, Wang S, Papp E, Bradshaw JM. Molecular mechanism of the Syk activation switch. The Journal of Biological Chemistry. 283: 32650-9. PMID 18818202 DOI: 10.1074/Jbc.M806340200 |
0.38 |
|
| 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 |
0.373 |
|
| 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 |
0.516 |
|
| 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 |
0.518 |
|
| 2007 |
Papp E, Tse JK, Ho H, Wang S, Shaw D, Lee S, Barnett J, Swinney DC, Bradshaw JM. Steady state kinetics of spleen tyrosine kinase investigated by a real time fluorescence assay. Biochemistry. 46: 15103-14. PMID 18052078 DOI: 10.1021/Bi701596U |
0.337 |
|
| 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 |
0.54 |
|
| 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 |
0.322 |
|
| 2007 |
Dinh M, Grunberger D, Ho H, Tsing SY, Shaw D, Lee S, Barnett J, Hill RJ, Swinney DC, Bradshaw JM. Activation mechanism and steady state kinetics of Bruton's tyrosine kinase. The Journal of Biological Chemistry. 282: 8768-76. PMID 17264076 DOI: 10.1074/Jbc.M609920200 |
0.361 |
|
| 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 |
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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 |
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