Autopalmitoylation of IDH1-R132H regulates its neomorphic activity in cancer cells L Hu, J Lin, L Sun, AM Berezuk, KS Tuttle, X Zhu, HS Seo, S Dhe-Paganon, P Li, Y Sun, L Ni, J Zhang, D Tan, H Wakimoto, DP Cahill, X Bai, X Luo, JM Asara, S Subramaniam, Y Shan, X Wu Nature Chemical Biology. DOI / Article
2025
Trillion Ligands per Day: Performance-Portable Virtual Screening via Compound Database Optimization and Multi-Target Docking X Duan, C Shen, G Chen, S Wu, Y Wang, Y Chen, Q Chang, Q Xia, Z Yin, L Gan, Y Shan, G Yang, W Liu, N Huang SC '25: The International Conference for High Performance Computing, Networking, Storage and Analysis. DOI / Article | Cited by 2
2024
BCR::ABL1 kinase N-lobe mutants confer moderate to high degrees of resistance to asciminib A Leyte-Vidal, DG Ruiz, R DeFilippis, IB Leske, D Rea, S Phan, KB Miller, F Hu, A Mase, Y Shan, O Hantschel, MP Jacobson, NP Shah Blood 144(6):639-645. DOI / Article | Cited by 35
Discovering Modulators of KRAS Nanoclustering JN Kapp, MJV Liste, G Nagy-Davidescu, S van Ruitenbeck, M Loza, J Brea, Y Shan, A Plückthun Mechanisms of Ras Oncogene Inhibition, 210.
Experimental variables determine the outcome of RAS-RAS interactions Z Zhou, TL Nguyen, X Li, C Poujol, E Berlinska, SV Michelina, JN Kapp, A Plückthun, MM Winslow, C Ambrogio, Y Shan, D Santamaría, KD Westover Journal of Biological Chemistry 300(11):107859. DOI / Article | Cited by 8
2023
Structural mechanism of a drug-binding process involving a large conformational change of the protein target P Ayaz, A Lyczek, Y Paung, VR Mingione, RE Iacob, PWd Waal, JR Engen, MA Seeliger, Y Shan, DE Shaw Nature Communications 14(1):1885. DOI / Article | Cited by 103
2022
How does a small molecule bind at a cryptic binding site? Y Shan, VP Mysore, AE Leffler, ET Kim, S Sagawa, DE Shaw PLOS Computational Biology 18(3):e1009817. DOI / Article | Cited by 52
Targetable HER3 functions driving tumorigenic signaling in HER2-amplified cancers MR Campbell, A Ruiz-Saenz, E Peterson, C Agnew, P Ayaz, S Garfinkle, P Littlefield, V Steri, J Oeffinger, M Sampang, Y Shan, DE Shaw, N Jura, MM Moasser Cell Reports 38(5):110291. DOI / Article | Cited by 20
Validation of an allosteric binding site of Src kinase identified by unbiased ligand binding simulations VR Mingione, ZH Foda, Y Paung, H Philipose, AM Rangwala, Y Shan, MA Seeliger Journal of molecular biology 434 (17), 167628. DOI / Article | Cited by 13
2021
A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation Y Liu, P Ke, YC Kuo, Y Wang, X Zhang, C Song, Y Shan eLife 10:e64304. DOI / Article | Cited by 10
A structural model of a Ras–Raf signalosome VP Mysore, ZW Zhou, C Ambrogio, L Li, JN Kapp, C Lu, Q Wang, MR Tucker, JJ Okoro, G Nagy-Davidescu, X Bai, A Plückthun, PA Jänne, KD Westover, Y Shan, DE Shaw Nature Structural & Molecular Biology 28(10):847-857. DOI / Article | Cited by 81
Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization C Agnew, P Ayaz, R Kashima, HS Loving, P Ghatpande, JE Kung, ES Underbakke, Y Shan, DE Shaw, A Hata, N Jura Nature Communications 12(1):4950. DOI / Article | Cited by 51
2020
Structural basis of AZD9291 selectivity for EGFR T790M XE Yan, P Ayaz, SJ Zhu, P Zhao, L Liang, CH Zhang, YC Wu, JL Li, HG Choi, X Huang, Y Shan, DE Shaw, CH Yun Journal of medicinal chemistry 63 (15), 8502-8511. DOI / Article | Cited by 117
2019
Structural models of full-length JAK2 kinase P Ayaz, HM Hammarén, J Raivola, D Sharon, SR Hubbard, O Silvennoinen, Y Shan, DE Shaw bioRxiv, 727727. DOI / Article | Cited by 8
2018
The architecture of EGFR's basal complexes reveals autoinhibition mechanisms in dimers and oligomers LC Zanetti-Domingues, D Korovesis, SR Needham, CJ Tynan, S Sagawa, A Arkhipov, VP Mysore, SK Roberts, ET Kim, V Losasso, DJ Clarke, M Hirsch, ML Martin-Fernandez, DT Clarke, AHA Clayton, M Perani, LJ Pike, PJ Parker, Y Shan, DE Shaw Nature communications 9 (1), 4325. DOI / Article | Cited by 96
2016
EGFR oligomerization organizes kinase-active dimers into competent signalling platforms SR Needham, SK Roberts, A Arkhipov, VP Mysore, CJ Tynan, LC Zanetti-Domingues, ET Kim, V Losasso, D Korovesis, M Hirsch, DJ Rolfe, DT Clarke, MD Winn, A Lajevardipour, AHA Clayton, LJ Pike, M Perani, PJ Parker, Y Shan, DE Shaw, ML Martin-Fernandez Nature Communications 7:13307. DOI / Article | Cited by 216
2015
A dynamically coupled allosteric network underlies binding cooperativity in Src kinase ZH Foda, Y Shan, ET Kim, DE Shaw, MA Seeliger Nature communications 6 (1), 5939. DOI / Article | Cited by 141
Allosteric activation of apicomplexan calcium-dependent protein kinases JR Ingram, KE Knockenhauer, BM Markus, J Mandelbaum, A Ramek, Y Shan, DE Shaw, TU Schwartz, HL Ploegh, S Lourido Proceedings of the National Academy of Sciences 112 (36), E4975-E4984. DOI / Article | Cited by 66
2014
Assessing the accuracy of two enhanced sampling methods using EGFR kinase transition pathways: the influence of collective variable choice AC Pan, TM Weinreich, Y Shan, DP Scarpazza, DE Shaw Journal of Chemical Theory and Computation 10 (7), 2860-2865. DOI / Article | Cited by 41
How IGF-1 activates its receptor JM Kavran, JM McCabe, PO Byrne, MK Connacher, Z Wang, A Ramek, S Sarabipour, Y Shan, DE Shaw, K Hristova, PA Cole, DJ Leahy Elife 3, e03772. DOI / Article | Cited by 244
IRAK4 dimerization and trans-autophosphorylation are induced by Myddosome assembly R Ferrao, H Zhou, Y Shan, Q Liu, Q Li, DE Shaw, X Li, H Wu Molecular cell 55 (6), 891-903. DOI / Article | Cited by 175
Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor A Arkhipov, Y Shan, ET Kim, DE Shaw PLoS computational biology 10 (7), e1003742. DOI / Article | Cited by 50
Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase Y Shan, K Gnanasambandan, D Ungureanu, ET Kim, H Hammarén, K Yamashita, O Silvennoinen, DE Shaw, SR Hubbard Nature structural & molecular biology 21 (7), 579-584. DOI / Article | Cited by 187
Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations P Littlefield, L Liu, V Mysore, Y Shan, DE Shaw, N Jura Science signaling 7 (354), ra114-ra114. DOI / Article | Cited by 149
2013
Architecture and membrane interactions of the EGF receptor A Arkhipov, Y Shan, R Das, NF Endres, MP Eastwood, DE Wemmer, J Kuriyan, DE Shaw Cell 152 (3), 557-569. DOI / Article | Cited by 610
Conformational coupling across the plasma membrane in activation of the EGF receptor NF Endres, R Das, AW Smith, A Arkhipov, E Kovacs, Y Huang, JG Pelton, Y Shan, DE Shaw, DE Wemmer, JT Groves, J Kuriyan Cell 152 (3), 543-556. DOI / Article | Cited by 584
Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family A Arkhipov, Y Shan, ET Kim, RO Dror, DE Shaw Elife 2, e00708. DOI / Article | Cited by 101
Transitions to catalytically inactive conformations in EGFR kinase Y Shan, A Arkhipov, ET Kim, AC Pan, DE Shaw Proceedings of the National Academy of Sciences 110 (18), 7270-7275. DOI / Article | Cited by 241
2012
Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F RM Bandaranayake, D Ungureanu, Y Shan, DE Shaw, O Silvennoinen, SR Hubbard Nature structural & molecular biology 19 (8), 754-759. DOI / Article | Cited by 305
Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization Y Shan, MP Eastwood, X Zhang, ET Kim, A Arkhipov, RO Dror, J Jumper, J Kuriyan, DE Shaw Cell 149 (4), 860-870. DOI / Article | Cited by 456
Regulation of RAS oncogenicity by acetylation MH Yang, S Nickerson, ET Kim, C Liot, G Laurent, R Spang, MR Philips, Y Shan, DE Shaw, D Bar-Sagi, MC Haigis, KM Haigis Proceedings of the National Academy of Sciences 109 (27), 10843-10848. DOI / Article | Cited by 154
2011
How does a drug molecule find its target binding site? Y Shan, ET Kim, MP Eastwood, RO Dror, MA Seeliger, DE Shaw Journal of the American Chemical Society 133 (24), 9181-9183. DOI / Article | Cited by 747
Pathway and mechanism of drug binding to G-protein-coupled receptors RO Dror, AC Pan, DH Arlow, DW Borhani, P Maragakis, Y Shan, H Xu, DE Shaw Proceedings of the National Academy of Sciences 108 (32), 13118-13123. DOI / Article | Cited by 893
2010
Atomic-level characterization of the structural dynamics of proteins DE Shaw, P Maragakis, K Lindorff-Larsen, S Piana, RO Dror, MP Eastwood, JA Bank, JM Jumper, JK Salmon, Y Shan, W Wriggers Science 330 (6002), 341-346. DOI / Article | Cited by 2335
2009
A conserved protonation-dependent switch controls drug binding in the Abl kinase Y Shan, MA Seeliger, MP Eastwood, F Frank, H Xu, MØ Jensen, RO Dror, J Kuriyan, DE Shaw Proceedings of the National Academy of Sciences 106 (1), 139-144. DOI / Article | Cited by 319
Automated event detection and activity monitoring in long molecular dynamics simulations W Wriggers, KA Stafford, Y Shan, S Piana, P Maragakis, K Lindorff-Larsen, PJ Miller, J Gullingsrud, CA Rendleman, MP Eastwood, RO Dror, DE Shaw Journal of chemical theory and computation 5 (10), 2595-2605. DOI / Article | Cited by 61
Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations MA Seeliger, P Ranjitkar, C Kasap, Y Shan, DE Shaw, NP Shah, J Kuriyan, DJ Maly Cancer research 69 (6), 2384-2392. DOI / Article | Cited by 190
Millisecond-scale molecular dynamics simulations on Anton DE Shaw, RO Dror, JK Salmon, JP Grossman, KM Mackenzie, JA Bank, C Young, MM Deneroff, B Batson, KJ Bowers, E Chow, MP Eastwood, D Ierardi, JL Klepeis, J Kuskin, RH Larson, K Lindorff-Larsen, P Maragakis, MA Moraes, S Piana, Y Shan, B Towles Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis. DOI / Article | Cited by 740
Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3 N Jura, Y Shan, X Cao, DE Shaw, J Kuriyan Proceedings of the National Academy of Sciences 106 (51), 21608-21613. DOI / Article | Cited by 410
2008
Anton, a special-purpose machine for molecular dynamics simulation DE Shaw, MM Deneroff, RO Dror, JS Kuskin, RH Larson, JK Salmon, C Young, B Batson, KJ Bowers, JC Chao, MP Eastwood, J Gagliardo, JP Grossman, CR Ho, DJ Ierardi, I Kolossvary, JL Klepeis, T Layman, C McLeavey, MA Moraes, R Mueller, EC Priest, Y Shan, J Spengler, M Theobald, B Towles, SC Wang Communications of the ACM 51 (7), 91-97. DOI / Article | Cited by 1053
High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation RH Larson, JK Salmon, RO Dror, MM Deneroff, C Young, JP Grossman, Y Shan, JL Klepeis, DE Shaw 2008 IEEE 14th International Symposium on High-Performance Computer Architecture. DOI / Article | Cited by 40
2007
Anton, a special-purpose machine for molecular dynamics simulation DE Shaw, MM Deneroff, RO Dror, JS Kuskin, RH Larson, JK Salmon, C Young, B Batson, KJ Bowers, JC Chao, MP Eastwood, J Gagliardo, JP Grossman, CR Ho, DJ Ierardi, I Kolossvary, JL Klepeis, T Layman, C McLeavey, MA Moraes, R Mueller, EC Priest, Y Shan, J Spengler, M Theobald, B Towles, SC Wang ACM SIGARCH Computer Architecture News 35 (2), 1-12. DOI / Article | Cited by 378
Mechanism of Na+/H+ antiporting IT Arkin, H Xu, MO Jensen, E Arbely, ER Bennett, KJ Bowers, E Chow, RO Dror, MP Eastwood, R Flitman-Tene, BA Gregersen, JL Klepeis, I Kolossvary, Y Shan, DE Shaw Science 317 (5839), 799-803. Cited by 184
2006
Scalable algorithms for molecular dynamics simulations on commodity clusters KJ Bowers, E Chow, H Xu, RO Dror, MP Eastwood, BA Gregersen, JL Klepeis, I Kolossvary, MA Moraes, FD Sacerdoti, JK Salmon, Y Shan, DE Shaw Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, 84-es. DOI / Article | Cited by 4427
2005
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation Y Shan, JL Klepeis, MP Eastwood, RO Dror, DE Shaw The Journal of chemical physics 122 (5), 054101. DOI / Article | Cited by 471
2001
Fold recognition and accurate query‐template alignment by a combination of PSI‐BLAST and threading Y Shan, G Wang, HX Zhou Proteins: Structure, Function, and Bioinformatics 42 (1), 23-37. DOI / Article | Cited by 47
Prediction of protein interaction sites from sequence profile and residue neighbor list HX Zhou, Y Shan Proteins: Structure, Function, and Bioinformatics 44 (3), 336-343. DOI / Article | Cited by 406
2000
Correspondence of potentials of mean force in proteins and in liquids Y Shan, HX Zhou The Journal of Chemical Physics 113 (11), 4794-4798. DOI / Article | Cited by 5