TY - BOOK AU - Berg, J. M. AU - Tymoczko, J. L. AU - Stryer, L. PY - 2002 DA - 2002// TI - Biochemistry PB - W.H. Freeman CY - New York ID - Berg2002 ER - TY - JOUR AU - Yutzey, K. E. AU - Colbert, M. AU - Robbins, J. PY - 2005 DA - 2005// TI - Ras-related signaling pathways in valve development: ebb and flow JO - Physiology (Bethesda) VL - 20 UR - https://doi.org/10.1152/physiol.00035.2005 DO - 10.1152/physiol.00035.2005 ID - Yutzey2005 ER - TY - JOUR AU - Lahiry, P. AU - Torkamani, A. AU - Schork, N. J. AU - Hegele, R. A. PY - 2010 DA - 2010// TI - Kinase mutations in human disease: interpreting genotype-phenotype relationships JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2707 DO - 10.1038/nrg2707 ID - Lahiry2010 ER - TY - JOUR AU - Macchi, P. AU - Villa, A. AU - Giliani, S. AU - Sacco, M. G. AU - Frattini, A. AU - Porta, F. AU - Ugazio, A. G. AU - Johnston, J. A. AU - Candotti, F. AU - O’Shea, J. J. PY - 1995 DA - 1995// TI - Mutations of Jak-3 gene in patients with autosomal severe combined immune deficiency (SCID) JO - Nature VL - 377 UR - https://doi.org/10.1038/377065a0 DO - 10.1038/377065a0 ID - Macchi1995 ER - TY - JOUR AU - Mosse, Y. P. AU - Wood, A. AU - Maris, J. M. PY - 2009 DA - 2009// TI - Inhibition of ALK signaling for cancer therapy JO - Clin Cancer Res VL - 15 UR - https://doi.org/10.1158/1078-0432.CCR-08-2762 DO - 10.1158/1078-0432.CCR-08-2762 ID - Mosse2009 ER - TY - JOUR AU - Hanks, S. K. AU - Hunter, T. PY - 1995 DA - 1995// TI - Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification JO - FASEB J VL - 9 ID - Hanks1995 ER - TY - JOUR AU - Cheng, H. C. AU - Qi, R. Z. AU - Paudel, H. AU - Zhu, H. J. PY - 2011 DA - 2011// TI - Regulation and function of protein kinases and phosphatases JO - Enzyme Res VL - 2011 UR - https://doi.org/10.4061/2011/794089 DO - 10.4061/2011/794089 ID - Cheng2011 ER - TY - JOUR AU - Huse, M. AU - Kuriyan, J. PY - 2002 DA - 2002// TI - The conformational plasticity of protein kinases JO - Cell VL - 109 UR - https://doi.org/10.1016/S0092-8674(02)00741-9 DO - 10.1016/S0092-8674(02)00741-9 ID - Huse2002 ER - TY - JOUR AU - Fang, Z. AU - Grutter, C. AU - Rauh, D. PY - 2013 DA - 2013// TI - Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features JO - ACS Chem Biol VL - 8 UR - https://doi.org/10.1021/cb300663j DO - 10.1021/cb300663j ID - Fang2013 ER - TY - JOUR AU - Adams, J. A. PY - 2003 DA - 2003// TI - Activation loop phosphorylation and catalysis in protein kinases: is there functional evidence for the autoinhibitor model? JO - Biochemistry VL - 42 UR - https://doi.org/10.1021/bi020617o DO - 10.1021/bi020617o ID - Adams2003 ER - TY - JOUR AU - Vulpetti, A. AU - Bosotti, R. PY - 2004 DA - 2004// TI - Sequence and structural analysis of kinase ATP pocket residues JO - Farmaco VL - 59 UR - https://doi.org/10.1016/j.farmac.2004.05.010 DO - 10.1016/j.farmac.2004.05.010 ID - Vulpetti2004 ER - TY - JOUR AU - Traxler, P. AU - Furet, P. PY - 1999 DA - 1999// TI - Strategies toward the design of novel and selective protein tyrosine kinase inhibitors JO - Pharmacol Ther VL - 82 UR - https://doi.org/10.1016/S0163-7258(98)00044-8 DO - 10.1016/S0163-7258(98)00044-8 ID - Traxler1999 ER - TY - JOUR AU - Liu, Y. AU - Shah, K. AU - Yang, F. AU - Witucki, L. AU - Shokat, K. M. PY - 1998 DA - 1998// TI - A molecular gate which controls unnatural ATP analogue recognition by the tyrosine kinase v-Src JO - Bioorg Med Chem VL - 6 UR - https://doi.org/10.1016/S0968-0896(98)00099-6 DO - 10.1016/S0968-0896(98)00099-6 ID - Liu1998 ER - TY - JOUR AU - Noble, M. E. M. AU - Endicott, J. A. AU - Johnson, L. N. PY - 2004 DA - 2004// TI - Protein kinase inhibitors: insights into drug design from structure JO - Science VL - 303 UR - https://doi.org/10.1126/science.1095920 DO - 10.1126/science.1095920 ID - Noble2004 ER - TY - JOUR AU - Azam, M. AU - Seeliger, M. A. AU - Gray, N. S. AU - Kuriyan, J. AU - Daley, G. Q. PY - 2008 DA - 2008// TI - Activation of tyrosine kinases by mutation of the gatekeeper threonine JO - Nat Struct Mol Biol VL - 15 UR - https://doi.org/10.1038/nsmb.1486 DO - 10.1038/nsmb.1486 ID - Azam2008 ER - TY - JOUR AU - Elphick, L. M. AU - Lee, S. E. AU - Gouverneur, V. AU - Mann, D. J. PY - 2007 DA - 2007// TI - Using chemical genetics and ATP analogues to dissect protein kinase function JO - ACS Chem Biol VL - 2 UR - https://doi.org/10.1021/cb700027u DO - 10.1021/cb700027u ID - Elphick2007 ER - TY - JOUR AU - Zuccotto, F. AU - Ardini, E. AU - Casale, E. AU - Angiolini, M. PY - 2010 DA - 2010// TI - Through the “gatekeeper door”: exploiting the active kinase conformation JO - J Med Chem VL - 53 UR - https://doi.org/10.1021/jm901443h DO - 10.1021/jm901443h ID - Zuccotto2010 ER - TY - JOUR AU - Huang, D. AU - Zhou, T. AU - Lafleur, K. AU - Nevado, C. AU - Caflisch, A. PY - 2010 DA - 2010// TI - Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp650 DO - 10.1093/bioinformatics/btp650 ID - Huang2010 ER - TY - JOUR AU - Shah, K. AU - Liu, Y. AU - Deirmengian, C. AU - Shokat, K. M. PY - 1997 DA - 1997// TI - Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.8.3565 DO - 10.1073/pnas.94.8.3565 ID - Shah1997 ER - TY - JOUR AU - Liu, Y. AU - Shah, K. AU - Yang, F. AU - Witucki, L. AU - Shokat, K. M. PY - 1998 DA - 1998// TI - Engineering Src family protein kinases with unnatural nucleotide specificity JO - Chem Biol VL - 5 UR - https://doi.org/10.1016/S1074-5521(98)90143-0 DO - 10.1016/S1074-5521(98)90143-0 ID - Liu1998 ER - TY - JOUR AU - Shah, K. AU - Shokat, K. M. PY - 2002 DA - 2002// TI - A chemical genetic screen for direct v-Src substrates reveals ordered assembly of a retrograde signaling pathway JO - Chem Biol VL - 9 UR - https://doi.org/10.1016/S1074-5521(02)00086-8 DO - 10.1016/S1074-5521(02)00086-8 ID - Shah2002 ER - TY - JOUR AU - Dephoure, N. AU - Howson, R. W. AU - Blethrow, J. D. AU - Shokat, K. M. AU - O’Shea, E. K. PY - 2005 DA - 2005// TI - Combining chemical genetics and proteomics to identify protein kinase substrates JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0509080102 DO - 10.1073/pnas.0509080102 ID - Dephoure2005 ER - TY - JOUR AU - Kraybill, B. C. AU - Elkin, L. L. AU - Blethrow, J. D. AU - Morgan, D. O. AU - Shokat, K. M. PY - 2002 DA - 2002// TI - Inhibitor scaffolds as new allele specific kinase substrates JO - J Am Chem Soc VL - 124 UR - https://doi.org/10.1021/ja0264798 DO - 10.1021/ja0264798 ID - Kraybill2002 ER - TY - JOUR AU - Larochelle, S. AU - Batliner, J. AU - Gamble, M. J. AU - Barboza, N. M. AU - Kraybill, B. C. AU - Blethrow, J. D. AU - Shokat, K. M. AU - Fisher, R. P. PY - 2006 DA - 2006// TI - Dichotomous but stringent substrate selection by the dual-function Cdk7 complex revealed by chemical genetics JO - Nat Struct Mol Biol VL - 13 UR - https://doi.org/10.1038/nsmb1028 DO - 10.1038/nsmb1028 ID - Larochelle2006 ER - TY - JOUR AU - Hindley, A. D. AU - Park, S. AU - Wang, L. AU - Shah, K. AU - Wang, Y. AU - Hu, X. AU - Shokat, K. M. AU - Kolch, W. AU - Sedivy, J. M. AU - Yeung, K. C. PY - 2004 DA - 2004// TI - Engineering the serine/threonine protein kinase Raf-1 to utilise an orthogonal analogue of ATP substituted at the N6 position JO - FEBS Lett VL - 556 UR - https://doi.org/10.1016/S0014-5793(03)01352-8 DO - 10.1016/S0014-5793(03)01352-8 ID - Hindley2004 ER - TY - JOUR AU - Habelhah, H. AU - Shah, K. AU - Huang, L. AU - Burlingame, A. L. AU - Shokat, K. M. AU - Ronai, Z. PY - 2001 DA - 2001// TI - Identification of new JNK substrate using ATP pocket mutant JNK and a corresponding ATP analogue JO - J Biol Chem VL - 276 UR - https://doi.org/10.1074/jbc.M011396200 DO - 10.1074/jbc.M011396200 ID - Habelhah2001 ER - TY - JOUR AU - Juris, S. J. AU - Shah, K. AU - Shokat, K. AU - Dixon, J. E. AU - Vacratsis, P. O. PY - 2006 DA - 2006// TI - Identification of otubain 1 as a novel substrate for the Yersinia protein kinase using chemical genetics and mass spectrometry JO - FEBS Lett VL - 580 UR - https://doi.org/10.1016/j.febslet.2005.11.071 DO - 10.1016/j.febslet.2005.11.071 ID - Juris2006 ER - TY - JOUR AU - Eblen, S. T. AU - Kumar, N. V. AU - Shah, K. AU - Henderson, M. J. AU - Watts, C. K. W. AU - Shokat, K. M. AU - Weber, M. J. PY - 2003 DA - 2003// TI - Identification of novel ERK2 substrates through use of an engineered kinase and ATP analogs JO - J Biol Chem VL - 278 UR - https://doi.org/10.1074/jbc.M300485200 DO - 10.1074/jbc.M300485200 ID - Eblen2003 ER - TY - JOUR AU - Chang, G. AU - Guida, W. C. AU - Still, W. C. PY - 1989 DA - 1989// TI - An internal coordinate monte-carlo method for searching conformational space JO - J Am Chem Soc VL - 111 UR - https://doi.org/10.1021/ja00194a035 DO - 10.1021/ja00194a035 ID - Chang1989 ER - TY - JOUR AU - Jorgensen, W. L. AU - Tiradorives, J. PY - 1988 DA - 1988// TI - The OPLS potential functions for proteins—energy minimizations for crystals of cyclic-peptides and crambin JO - J Am Chem Soc VL - 110 UR - https://doi.org/10.1021/ja00214a001 DO - 10.1021/ja00214a001 ID - Jorgensen1988 ER - TY - JOUR AU - Kaminski, G. A. AU - Friesner, R. A. AU - Tirado-Rives, J. AU - Jorgensen, W. L. PY - 2001 DA - 2001// TI - Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides JO - J Phys Chem B VL - 105 UR - https://doi.org/10.1021/jp003919d DO - 10.1021/jp003919d ID - Kaminski2001 ER - TY - JOUR AU - Allen, F. H. PY - 2002 DA - 2002// TI - The Cambridge Structural Database: a quarter of a million crystal structures and rising JO - Acta Crystallogr B VL - 58 UR - https://doi.org/10.1107/S0108768102003890 DO - 10.1107/S0108768102003890 ID - Allen2002 ER - TY - JOUR AU - Biasini, M. AU - Schmidt, T. AU - Bienert, S. AU - Mariani, V. AU - Studer, G. AU - Haas, J. AU - Johner, N. AU - Schenk, A. D. AU - Philippsen, A. AU - Schwede, T. PY - 2013 DA - 2013// TI - OpenStructure: an integrated software framework for computational structural biology JO - Acta Crystallogr D Biol Crystallogr VL - 69 UR - https://doi.org/10.1107/S0907444913007051 DO - 10.1107/S0907444913007051 ID - Biasini2013 ER - TY - JOUR AU - Sastry, G. M. AU - Adzhigirey, M. AU - Day, T. AU - Annabhimoju, R. AU - Sherman, W. PY - 2013 DA - 2013// TI - Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments JO - J Comput Aided Mol Des VL - 27 UR - https://doi.org/10.1007/s10822-013-9644-8 DO - 10.1007/s10822-013-9644-8 ID - Sastry2013 ER - TY - JOUR AU - Friesner, R. A. AU - Banks, J. L. AU - Murphy, R. B. AU - Halgren, T. A. AU - Klicic, J. J. AU - Mainz, D. T. AU - Repasky, M. P. AU - Knoll, E. H. AU - Shelley, M. AU - Perry, J. K. PY - 2004 DA - 2004// TI - Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy JO - J Med Chem VL - 47 UR - https://doi.org/10.1021/jm0306430 DO - 10.1021/jm0306430 ID - Friesner2004 ER - TY - JOUR AU - Colibus, L. AU - Wang, X. AU - Spyrou, J. A. AU - Kelly, J. AU - Ren, J. AU - Grimes, J. AU - Puerstinger, G. AU - Stonehouse, N. AU - Walter, T. S. AU - Hu, Z. PY - 2014 DA - 2014// TI - More-powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules JO - Nat Struct Mol Biol VL - 21 UR - https://doi.org/10.1038/nsmb.2769 DO - 10.1038/nsmb.2769 ID - Colibus2014 ER - TY - JOUR AU - Xie, X. AU - Gu, Y. AU - Fox, T. AU - Coll, J. T. AU - Fleming, M. A. AU - Markland, W. AU - Caron, P. R. AU - Wilson, K. P. AU - Su, M. S. PY - 1998 DA - 1998// TI - Crystal structure of JNK3: a kinase implicated in neuronal apoptosis JO - Structure VL - 6 UR - https://doi.org/10.1016/S0969-2126(98)00100-2 DO - 10.1016/S0969-2126(98)00100-2 ID - Xie1998 ER - TY - JOUR AU - Xu, W. AU - Doshi, A. AU - Lei, M. AU - Eck, M. J. AU - Harrison, S. C. PY - 1999 DA - 1999// TI - Crystal structures of c-Src reveal features of its autoinhibitory mechanism JO - Mol Cell VL - 3 UR - https://doi.org/10.1016/S1097-2765(00)80356-1 DO - 10.1016/S1097-2765(00)80356-1 ID - Xu1999 ER - TY - JOUR AU - Schindler, T. AU - Sicheri, F. AU - Pico, A. AU - Gazit, A. AU - Levitzki, A. AU - Kuriyan, J. PY - 1999 DA - 1999// TI - Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor JO - Mol Cell VL - 3 UR - https://doi.org/10.1016/S1097-2765(00)80357-3 DO - 10.1016/S1097-2765(00)80357-3 ID - Schindler1999 ER - TY - JOUR AU - Kinoshita, T. AU - Matsubara, M. AU - Ishiguro, H. AU - Okita, K. AU - Tada, T. PY - 2006 DA - 2006// TI - Structure of human Fyn kinase domain complexed with staurosporine JO - Biochem Biophys Res Commun VL - 346 UR - https://doi.org/10.1016/j.bbrc.2006.05.212 DO - 10.1016/j.bbrc.2006.05.212 ID - Kinoshita2006 ER - TY - JOUR AU - Levinson, N. M. AU - Kuchment, O. AU - Shen, K. AU - Young, M. A. AU - Koldobskiy, M. AU - Karplus, M. AU - Cole, P. A. AU - Kuriyan, J. PY - 2006 DA - 2006// TI - A Src-like inactive conformation in the abl tyrosine kinase domain JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040144 DO - 10.1371/journal.pbio.0040144 ID - Levinson2006 ER - TY - JOUR AU - Rellos, P. AU - Pike, A. C. W. AU - Niesen, F. H. AU - Salah, E. AU - Lee, W. H. AU - Delft, F. AU - Knapp, S. PY - 2010 DA - 2010// TI - Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation JO - PLoS Biol VL - 8 UR - https://doi.org/10.1371/journal.pbio.1000426 DO - 10.1371/journal.pbio.1000426 ID - Rellos2010 ER - TY - JOUR AU - Schulze-Gahmen, U. AU - Bondt, H. L. AU - Kim, S. H. PY - 1996 DA - 1996// TI - High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: bound waters and natural ligand as guides for inhibitor design JO - J Med Chem VL - 39 UR - https://doi.org/10.1021/jm960402a DO - 10.1021/jm960402a ID - Schulze-Gahmen1996 ER - TY - JOUR AU - Shewchuk, L. AU - Hassell, A. AU - Wisely, B. AU - Rocque, W. AU - Holmes, W. AU - Veal, J. AU - Kuyper, L. F. PY - 2000 DA - 2000// TI - Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase JO - J Med Chem VL - 43 UR - https://doi.org/10.1021/jm990401t DO - 10.1021/jm990401t ID - Shewchuk2000 ER - TY - JOUR AU - Polak, E. R. G. PY - 1969 DA - 1969// TI - Note sur la convergence de methodes de directions conjugees JO - Revenue Francaise Informat Recherce Operationelle, Serie Rouge VL - 3 ID - Polak1969 ER - TY - JOUR AU - Hunter, J. D. PY - 2007 DA - 2007// TI - Matplotlib: a 2D graphics environment JO - Comput Sci Eng VL - 9 UR - https://doi.org/10.1109/MCSE.2007.55 DO - 10.1109/MCSE.2007.55 ID - Hunter2007 ER - TY - JOUR AU - Walt, S. AU - Colbert, S. C. AU - Varoquaux, G. PY - 2011 DA - 2011// TI - The NumPy array: a structure for efficient numerical computation JO - Comput Sci Eng VL - 13 UR - https://doi.org/10.1109/MCSE.2011.37 DO - 10.1109/MCSE.2011.37 ID - Walt2011 ER - TY - JOUR AU - Liu, Y. AU - Bishop, A. AU - Witucki, L. AU - Kraybill, B. AU - Shimizu, E. AU - Tsien, J. AU - Ubersax, J. AU - Blethrow, J. AU - Morgan, D. O. AU - Shokat, K. M. PY - 1999 DA - 1999// TI - Structural basis for selective inhibition of Src family kinases by PP1 JO - Chem Biol VL - 6 UR - https://doi.org/10.1016/S1074-5521(99)80118-5 DO - 10.1016/S1074-5521(99)80118-5 ID - Liu1999 ER - TY - JOUR AU - Buzko, O. V. AU - Bishop, A. C. AU - Shokat, K. M. PY - 2002 DA - 2002// TI - Modified AutoDock for accurate docking of protein kinase inhibitors JO - J Comput Aided Mol Des VL - 16 UR - https://doi.org/10.1023/A:1016366013656 DO - 10.1023/A:1016366013656 ID - Buzko2002 ER - TY - JOUR AU - Cravatt, B. F. PY - 2005 DA - 2005// TI - Kinase chemical genomics–a new rule for the exceptions JO - Nat Methods VL - 2 UR - https://doi.org/10.1038/nmeth0605-411 DO - 10.1038/nmeth0605-411 ID - Cravatt2005 ER - TY - JOUR AU - Bucci, M. AU - Goodman, C. AU - Sheppard, T. L. PY - 2010 DA - 2010// TI - A decade of chemical biology JO - Nat Chem Biol VL - 6 UR - https://doi.org/10.1038/nchembio.489 DO - 10.1038/nchembio.489 ID - Bucci2010 ER - TY - JOUR AU - Tommaso, P. AU - Moretti, S. AU - Xenarios, I. AU - Orobitg, M. AU - Montanyola, A. AU - Chang, J. M. AU - Taly, J. F. AU - Notredame, C. PY - 2011 DA - 2011// TI - T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr245 DO - 10.1093/nar/gkr245 ID - Tommaso2011 ER -