Yibing Shan
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Scalable algorithms for molecular dynamics simulations on commodity clusters
KJ Bowers, DE Chow, H Xu, RO Dror, MP Eastwood, BA Gregersen, ...
SC'06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, 43-43, 2006
Atomic-level characterization of the structural dynamics of proteins
DE Shaw, P Maragakis, K Lindorff-Larsen, S Piana, RO Dror, ...
Science 330 (6002), 341-346, 2010
Anton, a special-purpose machine for molecular dynamics simulation
DE Shaw, MM Deneroff, RO Dror, JS Kuskin, RH Larson, JK Salmon, ...
Communications of the ACM 51 (7), 91-97, 2008
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, ...
Proceedings of the National Academy of Sciences 108 (32), 13118-13123, 2011
Millisecond-scale molecular dynamics simulations on Anton
DE Shaw, RO Dror, JK Salmon, JP Grossman, KM Mackenzie, JA Bank, ...
Proceedings of the conference on high performance computing networking…, 2009
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, 2011
Architecture and membrane interactions of the EGF receptor
A Arkhipov, Y Shan, R Das, NF Endres, MP Eastwood, DE Wemmer, ...
Cell 152 (3), 557-569, 2013
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, ...
Cell 152 (3), 543-556, 2013
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, 2001
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, 2005
Anton, a special-purpose machine for molecular dynamics simulation
DE Shaw, MM Deneroff, RO Dror, JS Kuskin, RH Larson, JK Salmon, ...
ACM SIGARCH Computer Architecture News 35 (2), 1-12, 2007
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, 2009
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, ...
Cell 149 (4), 860-870, 2012
A conserved protonation-dependent switch controls drug binding in the Abl kinase
Y Shan, MA Seeliger, MP Eastwood, F Frank, H Xu, M Jensen, RO Dror, ...
Proceedings of the National Academy of Sciences 106 (1), 139-144, 2009
Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F
RM Bandaranayake, D Ungureanu, Y Shan, DE Shaw, O Silvennoinen, ...
Nature structural & molecular biology 19 (8), 754-759, 2012
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, 2013
Mechanism of Na+/H+ antiporting
IT Arkin, H Xu, M Jensen, E Arbely, ER Bennett, KJ Bowers, E Chow, ...
Science 317 (5839), 799-803, 2007
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, ...
Cancer research 69 (6), 2384-2392, 2009
How IGF-1 activates its receptor
JM Kavran, JM McCabe, PO Byrne, MK Connacher, Z Wang, A Ramek, ...
Elife 3, e03772, 2014
Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase
Y Shan, K Gnanasambandan, D Ungureanu, ET Kim, H Hammarn, ...
Nature structural & molecular biology 21 (7), 579-584, 2014
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