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yibing shan, Ph.D - Publications

Affiliations: 
2002- D. E. Shaw Research, New York, NY, United States 
Area:
Computational biophysics and biology
Website:
http://www.csrc.ac.cn/~ybshan/
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45 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
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  0.554
2022 Mingione VR, Foda ZH, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. Validation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations. Journal of Molecular Biology. 167628. PMID 35595169 DOI: 10.1016/j.jmb.2022.167628  0.3
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  0.451
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  0.517
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, 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  0.427
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  0.518
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  0.591
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, ... ... Shan Y, 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  0.584
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  0.544
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, ... ... Shan Y, et al. EGFR oligomerization organizes kinase-active dimers into competent signalling platforms. Nature Communications. 7: 13307. PMID 27796308 DOI: 10.1038/Ncomms13307  0.601
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  0.563
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  0.578
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  0.539
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  0.605
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  0.541
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  0.594
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  0.583
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  0.59
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  0.474
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  0.461
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  0.439
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  0.589
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  0.621
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  0.601
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  0.535
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  0.497
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  0.509
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  0.581
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  0.466
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  0.592
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  0.516
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  0.556
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  0.52
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  0.528
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  0.598
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  0.559
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  0.591
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, ... ... Shan Y, 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  0.413
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  0.429
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  0.516
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, ... ... Shan Y, et al. Anton, a special-purpose machine for molecular dynamics simulation Communications of the Acm. 51: 91-97. DOI: 10.1145/1364782.1364802  0.41
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  0.413
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  0.461
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  0.383
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  0.412
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