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albanese.bib
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@article{respa,
author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
title = {Reversible multiple time scale molecular dynamics},
journal = {The Journal of Chemical Physics},
volume = {97},
number = {3},
pages = {1990-2001},
year = {1992},
doi = {10.1063/1.463137},
URL = {
https://doi.org/10.1063/1.463137
},
eprint = {
https://doi.org/10.1063/1.463137
}
}
@article{pme,
author = {Ulrich Essmann and Lalith Perera and Max L. Berkowitz and Tom Darden and Hsing Lee and Lee G. Pedersen},
title = {A smooth particle mesh Ewald method},
journal = {The Journal of Chemical Physics},
volume = {103},
number = {19},
pages = {8577-8593},
year = {1995},
doi = {10.1063/1.470117},
URL = {
https://doi.org/10.1063/1.470117
},
eprint = {
https://doi.org/10.1063/1.470117
}
}
@article{hmr,
author = {Hopkins, Chad W. and Le Grand, Scott and Walker, Ross C. and Roitberg, Adrian E.},
title = {Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning},
journal = {Journal of Chemical Theory and Computation},
volume = {11},
number = {4},
pages = {1864-1874},
year = {2015},
doi = {10.1021/ct5010406},
note ={PMID: 26574392},
URL = {
http://dx.doi.org/10.1021/ct5010406
},
eprint = {
http://dx.doi.org/10.1021/ct5010406
}
}
@article{mtk,
author = {Glenn J. Martyna and Douglas J. Tobias and Michael L. Klein},
title = {Constant pressure molecular dynamics algorithms},
journal = {The Journal of Chemical Physics},
volume = {101},
number = {5},
pages = {4177-4189},
year = {1994},
doi = {10.1063/1.467468},
URL = {
https://doi.org/10.1063/1.467468
},
eprint = {
https://doi.org/10.1063/1.467468
}
}
@article{langevin-piston,
author = {Scott E. Feller and Yuhong Zhang and Richard W. Pastor and Bernard R. Brooks},
title = {Constant pressure molecular dynamics simulation: The Langevin piston method},
journal = {The Journal of Chemical Physics},
volume = {103},
number = {11},
pages = {4613-4621},
year = {1995},
doi = {10.1063/1.470648},
URL = {
https://doi.org/10.1063/1.470648
},
eprint = {
https://doi.org/10.1063/1.470648
}
}
@article{pymc3,
title = {Probabilistic programming in Python using PyMC3},
author = {Salvatier, John and Wiecki, Thomas V. and Fonnesbeck, Christopher},
year = 2016,
month = apr,
keywords = {Bayesian statistic, Probabilistic Programming, Python, Markov chain Monte Carlo, Statistical modeling},
abstract = {
Probabilistic programming allows for automatic Bayesian inference on user-defined probabilistic models. Recent advances in Markov chain Monte Carlo (MCMC) sampling allow inference on increasingly complex models. This class of MCMC, known as Hamiltonian Monte Carlo, requires gradient information which is often not readily available. PyMC3 is a new open source probabilistic programming framework written in Python that uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed. Contrary to other probabilistic programming languages, PyMC3 allows model specification directly in Python code. The lack of a domain specific language allows for great flexibility and direct interaction with the model. This paper is a tutorial-style introduction to this software package.
},
volume = 2,
pages = {e55},
journal = {PeerJ Computer Science},
issn = {2376-5992},
url = {https://doi.org/10.7717/peerj-cs.55},
doi = {10.7717/peerj-cs.55}
}
@article{BUCZEK201431,
title = "Resistance to tyrosine kinase inhibitors in clear cell renal cell carcinoma: From the patient's bed to molecular mechanisms",
journal = "Biochimica et Biophysica Acta (BBA) - Reviews on Cancer",
volume = "1845",
number = "1",
pages = "31 - 41",
year = "2014",
issn = "0304-419X",
doi = "https://doi.org/10.1016/j.bbcan.2013.10.001",
url = "http://www.sciencedirect.com/science/article/pii/S0304419X13000437",
author = "Magdalena Buczek and Bernard Escudier and Ewa Bartnik and Cezary Szczylik and Anna Czarnecka",
keywords = "Clear cell renal cell carcinoma, Tyrosine kinase inhibitors, Drug resistance, Angiogenesis, Acquired and intrinsic resistance"
}
@article{Chandarlapaty:CancerCell:2011,
title = {{{AKT Inhibition Relieves Feedback Suppression}} of {{Receptor Tyrosine Kinase Expression}} and {{Activity}}},
volume = {19},
issn = {15356108},
doi = {10.1016/j.ccr.2010.10.031},
language = {en},
timestamp = {2014-09-14T14:05:22Z},
number = {1},
urldate = {2014-09-14},
journal = {Cancer Cell},
author = {Chandarlapaty, Sarat and Sawai, Ayana and Scaltriti, Maurizio and Rodrik-Outmezguine, Vanessa and Grbovic-Huezo, Olivera and Serra, Violeta and Majumder, Pradip K. and Baselga, Jose and Rosen, Neal},
month = jan,
year = {2011},
pages = {58--71},
file = {1-s2.0-S1535610810004332-main.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/F6HCHU8B/1-s2.0-S1535610810004332-main.pdf:application/pdf}
}
@article{Martin:2009:JournalofComputer-AidedMolecularDesign,
title = {Let's Not Forget Tautomers},
volume = {23},
issn = {0920-654X, 1573-4951},
doi = {10.1007/s10822-009-9303-2},
language = {en},
timestamp = {2014-09-14T14:10:31Z},
number = {10},
urldate = {2014-09-14},
journal = {J. Comput. Aided Mol. Des.},
author = {Martin, Yvonne Connolly},
month = oct,
year = {2009},
pages = {693--704},
file = {art%3A10.1007%2Fs10822-009-9303-2.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/27TJH2BE/art%3A10.1007%2Fs10822-009-9303-2.pdf:application/pdf}
}
@article{Reif:J.Comput.Chem.:2014,
title = {Net Charge Changes in the Calculation of Relative Ligand-Binding Free Energies via Classical Atomistic Molecular Dynamics Simulation},
volume = {35},
issn = {01928651},
doi = {10.1002/jcc.23490},
language = {en},
timestamp = {2014-09-14T14:17:22Z},
number = {3},
urldate = {2014-09-14},
journal = {J. Comput. Chem.},
author = {Reif, Maria M. and Oostenbrink, Chris},
month = jan,
year = {2014},
pages = {227--243},
file = {jcc23490.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/T36Z8CNK/jcc23490.pdf:application/pdf}
}
@article{Foda:Nat.Commun.:2015,
title = {A Dynamically Coupled Allosteric Network Underlies Binding Cooperativity in {{Src}} Kinase},
volume = {6},
issn = {2041-1723},
doi = {10.1038/ncomms6939},
timestamp = {2015-03-22T03:12:53Z},
urldate = {2015-03-22},
journal = {Nat. Commun.},
author = {Foda, Zachariah H. and Shan, Yibing and Kim, Eric T. and Shaw, David E. and Seeliger, Markus A.},
month = jan,
year = {2015},
pages = {5939},
file = {ncomms6939.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/E5KF8I3W/ncomms6939.pdf:application/pdf}
}
@article{Shelley:J.Comput.AidedMol.Des.:2007,
title = {Epik: A Software Program for {{pK}} a Prediction and Protonation State Generation for Drug-like Molecules},
volume = {21},
issn = {0920-654X, 1573-4951},
shorttitle = {Epik},
doi = {10.1007/s10822-007-9133-z},
language = {en},
timestamp = {2015-04-14T18:33:12Z},
number = {12},
urldate = {2015-04-14},
journal = {J. Comput. Aided Mol. Des.},
author = {Shelley, John C. and Cholleti, Anuradha and Frye, Leah L. and Greenwood, Jeremy R. and Timlin, Mathew R. and Uchimaya, Makoto},
month = dec,
year = {2007},
pages = {681--691},
file = {art%3A10.1007%2Fs10822-007-9133-z.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/NKQ4VRPM/art%3A10.1007%2Fs10822-007-9133-z.pdf:application/pdf}
}
@article{Davis:Nat.Biotechnol.:2011,
title = {Comprehensive Analysis of Kinase Inhibitor Selectivity},
volume = {29},
issn = {1087-0156, 1546-1696},
doi = {10.1038/nbt.1990},
timestamp = {2015-06-22T19:06:43Z},
number = {11},
urldate = {2015-06-22},
journal = {Nat. Biotechnol.},
author = {Davis, Mindy I and Hunt, Jeremy P and Herrgard, Sanna and Ciceri, Pietro and Wodicka, Lisa M and Pallares, Gabriel and Hocker, Michael and Treiber, Daniel K and Zarrinkar, Patrick P},
month = oct,
year = {2011},
pages = {1046--1051},
file = {nbt.1990.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/QXIDV8ZZ/nbt.1990.pdf:application/pdf}
}
@article{Kramer:J.Med.Chem.:2012,
title = {The {{Experimental Uncertainty}} of {{Heterogeneous Public}} {{{\emph{K}}}} {\textsubscript{i}} {{Data}}},
volume = {55},
issn = {0022-2623, 1520-4804},
doi = {10.1021/jm300131x},
language = {en},
timestamp = {2015-08-20T20:35:48Z},
number = {11},
urldate = {2015-08-20},
journal = {J. Med. Chem.},
author = {Kramer, Christian and Kalliokoski, Tuomo and Gedeck, Peter and Vulpetti, Anna},
month = jun,
year = {2012},
pages = {5165--5173},
file = {jm300131x.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/APU7XWNP/jm300131x.pdf:application/pdf}
}
@article{Shah:CancerCell:2002,
title = {Multiple {{BCR}}-{{ABL}} Kinase Domain Mutations Confer Polyclonal Resistance to the Tyrosine Kinase Inhibitor Imatinib ({{STI571}}) in Chronic Phase and Blast Crisis Chronic Myeloid Leukemia},
volume = {2},
issn = {1535-6108},
abstract = {Through sequencing analysis of blood or bone marrow samples from patients with chronic myeloid leukemia, we identified BCR-ABL kinase domain mutations in 29 of 32 patients whose disease relapsed after an initial response to the tyrosine kinase inhibitor imatinib. Fifteen different amino acid substitutions affecting 13 residues in the kinase domain were found. Mutations fell into two groups-those that alter amino acids that directly contact imatinib and those postulated to prevent BCR-ABL from achieving the inactive conformational state required for imatinib binding. Distinct mutations conferred varying degrees of imatinib resistance. Mutations detected in a subset of patients with stable chronic phase disease correlated with subsequent disease progression. Multiple independent mutant clones were detected in a subset of relapsed cases. Our data support a clonal selection model of preexisting BCR-ABL mutations that confer imatinib resistance.},
language = {eng},
timestamp = {2015-09-25T13:18:12Z},
number = {2},
journal = {Cancer Cell},
author = {Shah, Neil P. and Nicoll, John M. and Nagar, Bhushan and Gorre, Mercedes E. and Paquette, Ronald L. and Kuriyan, John and Sawyers, Charles L.},
month = aug,
year = {2002},
keywords = {Alleles,Amino Acid Sequence,Antineoplastic Agents,Benzamides,Clinical Trials as Topic,Clone Cells,DNA Mutational Analysis,Drug Resistance; Neoplasm,Fusion Proteins; bcr-abl,Humans,Leukemia; Myelogenous; Chronic; BCR-ABL Positive,Models; Molecular,Mutation,Neoplasm Recurrence; Local,Piperazines,Protein Structure; Tertiary,Pyrimidines,Recurrence,Time Factors},
pages = {117--125},
file = {PIIS153561080200096X.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/M6XRQ8S2/PIIS153561080200096X.pdf:application/pdf},
pmid = {12204532}
}
@article{Neal:Stat.Comput.:2001,
title = {Equilibrium {{Free Energies}} from {{Nonequilibrium Measurements Using Maximum}}-{{Likelihood Methods}}},
volume = {91},
issn = {0031-9007, 1079-7114},
doi = {10.1103/PhysRevLett.91.140601},
language = {en},
timestamp = {2015-09-27T23:25:33Z},
number = {14},
urldate = {2015-09-27},
journal = {Phys. Rev. Lett.},
author = {Shirts, Michael R. and Bair, Eric and Hooker, Giles and Pande, Vijay S.},
month = oct,
year = {2003}
}
@article{Shirts:J.Phys.Chem.B:2007,
title = {Accurate and {{Efficient Corrections}} for {{Missing Dispersion Interactions}} in {{Molecular Simulations}}},
volume = {111},
issn = {1520-6106, 1520-5207},
doi = {10.1021/jp0735987},
language = {en},
timestamp = {2015-10-26T22:40:41Z},
number = {45},
urldate = {2014-09-14},
journal = {J. Phys. Chem. B},
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
month = nov,
year = {2007},
pages = {13052--13063},
file = {J Phys Chem B 2007 Shirts.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/2UA54DF8/J Phys Chem B 2007 Shirts.pdf:application/pdf;J Phys Chem B 2007 Shirts-1.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/8IZ27J6D/J Phys Chem B 2007 Shirts-1.pdf:application/pdf;jp0735987.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/9NQTRUUS/jp0735987.pdf:application/pdf;J Phys Chem B 2007 Shirts.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/BHNJNCE2/J Phys Chem B 2007 Shirts.pdf:application/pdf;J Phys Chem B 2007 Shirts-1.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/TKCXJPEV/J Phys Chem B 2007 Shirts-1.pdf:application/pdf}
}
@article{Chodera:Curr.Opin.Struct.Biol.:2011,
title = {Alchemical Free Energy Methods for Drug Discovery: Progress and Challenges},
volume = {21},
issn = {0959440X},
shorttitle = {Alchemical Free Energy Methods for Drug Discovery},
doi = {10.1016/j.sbi.2011.01.011},
language = {en},
timestamp = {2015-10-26T22:41:16Z},
number = {2},
urldate = {2015-03-22},
journal = {Curr. Opin. Struct. Biol.},
author = {Chodera, John D and Mobley, David L and Shirts, Michael R and Dixon, Richard W and Branson, Kim and Pande, Vijay S},
month = apr,
year = {2011},
pages = {150--160},
file = {Curr. Opin. Struct. Biol. 2011 Chodera.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/J6WXPE7H/Curr. Opin. Struct. Biol. 2011 Chodera.pdf:application/pdf;Curr. Opin. Struct. Biol. 2011 Chodera.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/XHUPBD64/Curr. Opin. Struct. Biol. 2011 Chodera.pdf:application/pdf}
}
@incollection{Shirts:AnnualReportsinComputationalChemistry:2007,
title = {Chapter 4 {{Alchemical Free Energy Calculations}}: {{Ready}} for {{Prime Time}}?},
volume = {3},
isbn = {978-0-444-53088-2},
shorttitle = {Chapter 4 {{Alchemical Free Energy Calculations}}},
language = {en},
timestamp = {2015-10-26T22:42:04Z},
urldate = {2014-09-14},
booktitle = {Annual {{Reports}} in {{Computational Chemistry}}},
publisher = {{Elsevier}},
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D.},
year = {2007},
pages = {41--59},
file = {alchemical-free-energy-review.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/D5JEE4M2/alchemical-free-energy-review.pdf:application/pdf;2007 Shirts.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/PRGJC67W/2007 Shirts.pdf:application/pdf;2007 Shirts.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/S9KGS6RA/2007 Shirts.pdf:application/pdf}
}
@article{Maier:J.Chem.TheoryComput.:2015,
title = {{{ff14SB}}: {{Improving}} the {{Accuracy}} of {{Protein Side Chain}} and {{Backbone Parameters}} from {{ff99SB}}},
volume = {11},
issn = {1549-9618, 1549-9626},
shorttitle = {{{ff14SB}}},
doi = {10.1021/acs.jctc.5b00255},
language = {en},
timestamp = {2016-02-07T20:15:04Z},
number = {8},
urldate = {2016-02-07},
journal = {J. Chem. Theory Comput.},
author = {Maier, James A. and Martinez, Carmenza and Kasavajhala, Koushik and Wickstrom, Lauren and Hauser, Kevin E. and Simmerling, Carlos},
month = aug,
year = {2015},
pages = {3696--3713},
file = {acs%2Ejctc%2E5b00255.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/UISVABBI/acs%2Ejctc%2E5b00255.pdf:application/pdf}
}
@article{Meng:J.Phys.Chem.B:2015,
title = {Computational {{Study}} of the ``{{DFG}}-{{Flip}}'' {{Conformational Transition}} in c-{{Abl}} and c-{{Src Tyrosine Kinases}}},
volume = {119},
issn = {1520-6106, 1520-5207},
doi = {10.1021/jp511792a},
language = {en},
timestamp = {2016-05-10T16:28:41Z},
number = {4},
urldate = {2016-05-10},
journal = {J. Phys. Chem. B},
author = {Meng, Yilin and Lin, Yen-lin and Roux, Beno{\^\i}t},
month = jan,
year = {2015},
pages = {1443--1456},
file = {jp511792a.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/NPDSFWK2/jp511792a.pdf:application/pdf}
}
@article{Shan:Proc.Natl.Acad.Sci.:2009,
title = {A Conserved Protonation-Dependent Switch Controls Drug Binding in the {{Abl}} Kinase},
volume = {106},
timestamp = {2016-05-10T16:28:44Z},
number = {1},
urldate = {2016-05-10},
journal = {Proc. Natl. Acad. Sci.},
author = {Shan, Yibing and Seeliger, Markus A. and Eastwood, Michael P. and Frank, Filipp and Xu, Huafeng and Jensen, Morten {\O} and Dror, Ron O. and Kuriyan, John and Shaw, David E.},
year = {2009},
pages = {139--144},
file = {PNAS-2009-Shan-139-44.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/AMQ5VDPR/PNAS-2009-Shan-139-44.pdf:application/pdf}
}
@article{Onufriev:Q.Rev.Biophys.:2013,
title = {Protonation and {{pK}} Changes in Protein\textendash{}ligand Binding},
volume = {46},
issn = {0033-5835, 1469-8994},
doi = {10.1017/S0033583513000024},
language = {en},
timestamp = {2016-09-26T22:07:57Z},
number = {02},
urldate = {2016-09-26},
journal = {Q. Rev. Biophys.},
author = {Onufriev, Alexey V. and Alexov, Emil},
month = may,
year = {2013},
pages = {181--209},
file = {nihms-591639.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/3IVRZT5N/nihms-591639.pdf:application/pdf}
}
@article{Lim:J.Chem.TheoryComput.:2016,
title = {Sensitivity in {{Binding Free Energies Due}} to {{Protein Reorganization}}},
volume = {12},
issn = {1549-9618},
doi = {10.1021/acs.jctc.6b00532},
abstract = {Tremendous recent improvements in computer hardware, coupled with advances in sampling techniques and force fields, are now allowing protein\textendash{}ligand binding free energy calculations to be routinely used to aid pharmaceutical drug discovery projects. However, despite these recent innovations, there are still needs for further improvement in sampling algorithms to more adequately sample protein motion relevant to protein\textendash{}ligand binding. Here, we report our work identifying and studying such clear and remaining needs in the apolar cavity of T4 lysozyme L99A. In this study, we model recent experimental results that show the progressive opening of the binding pocket in response to a series of homologous ligands.1 Even while using enhanced sampling techniques, we demonstrate that the predicted relative binding free energies (RBFE) are sensitive to the initial protein conformational state. Particularly, we highlight the importance of sufficient sampling of protein conformational changes and demonstrate how inclusion of three key protein residues in the ``hot'' region of the FEP/REST simulation improves the sampling and resolves this sensitivity, given enough simulation time.},
timestamp = {2016-11-16T16:26:56Z},
number = {9},
urldate = {2016-11-16},
journal = {J. Chem. Theory Comput.},
author = {Lim, Nathan M. and Wang, Lingle and Abel, Robert and Mobley, David L.},
month = sep,
year = {2016},
pages = {4620--4631},
file = {ACS Full Text PDF w/ Links:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/ZN2K4S9Z/Lim et al. - 2016 - Sensitivity in Binding Free Energies Due to Protei.pdf:application/pdf;ACS Full Text Snapshot:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/MMIVXW88/acs.jctc.html:text/html}
}
@article{Santos:Nat.Rev.DrugDiscov.:2016,
title = {A Comprehensive Map of Molecular Drug Targets},
volume = {16},
issn = {1474-1776, 1474-1784},
doi = {10.1038/nrd.2016.230},
timestamp = {2017-06-25T02:12:18Z},
number = {1},
urldate = {2017-06-25},
journal = {Nat. Rev. Drug Discov.},
author = {Santos, Rita and Ursu, Oleg and Gaulton, Anna and Bento, A. Patr?cia and Donadi, Ramesh S. and Bologa, Cristian G. and Karlsson, Anneli and Al-Lazikani, Bissan and Hersey, Anne and Oprea, Tudor I. and Overington, John P.},
month = dec,
year = {2016},
pages = {19--34},
file = {nrd.2016.230.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/JCTGUBFC/nrd.2016.230.pdf:application/pdf}
}
@article{fda-approved-kinase-inhibitors,
title = {{{USFDA}} Approved Protein Kinase Inhibitors},
timestamp = {2017-06-25T21:47:01Z},
author = {{Robert Roskoski Jr}},
year = {2017},
note = {Updated 3 May 2017},
url = {http://www.brimr.org/PKI/PKIs.htm},
}
@article{Kalliokoski:PloSOne:2013,
title = {Comparability of Mixed {{IC50}} Data\textendash{}a Statistical Analysis},
volume = {8},
timestamp = {2017-08-08T11:33:35Z},
number = {4},
urldate = {2017-08-08},
journal = {PloS One},
author = {Kalliokoski, Tuomo and Kramer, Christian and Vulpetti, Anna and Gedeck, Peter},
year = {2013},
pages = {e61007},
file = {journal.pone.0061007.PDF:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/8INQD8BE/journal.pone.0061007.PDF:application/pdf}
}
@article{Housman:Cancers:2014,
title = {Drug {{Resistance}} in {{Cancer}}: {{An Overview}}},
volume = {6},
issn = {2072-6694},
shorttitle = {Drug {{Resistance}} in {{Cancer}}},
doi = {10.3390/cancers6031769},
language = {en},
timestamp = {2017-08-10T10:35:28Z},
number = {3},
urldate = {2017-08-10},
journal = {Cancers},
author = {Housman, Genevieve and Byler, Shannon and Heerboth, Sarah and Lapinska, Karolina and Longacre, Mckenna and Snyder, Nicole and Sarkar, Sibaji},
month = sep,
year = {2014},
pages = {1769--1792},
file = {cancers-06-01769.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/U5U92BVZ/cancers-06-01769.pdf:application/pdf}
}
@article{Gruber:Med.Oncol.:2012,
title = {{{BCR}}-{{ABL}} Isoforms Associated with Intrinsic or Acquired Resistance to Imatinib: More Heterogeneous than Just {{ABL}} Kinase Domain Point Mutations?},
volume = {29},
issn = {1357-0560, 1559-131X},
shorttitle = {{{BCR}}-{{ABL}} Isoforms Associated with Intrinsic or Acquired Resistance to Imatinib},
doi = {10.1007/s12032-010-9781-z},
language = {en},
timestamp = {2017-08-27T20:38:01Z},
number = {1},
urldate = {2017-08-27},
journal = {Med. Oncol.},
author = {Gruber, Franz X. and Lund{\'a}n, Tuija and Goll, Rasmus and Silye, Aleksandra and Mikkola, Ingvild and Rekvig, Ole Petter and Knuutila, Sakari and Remes, Kari and Gedde-Dahl, Tobias and Porkka, Kimmo and Hjorth-Hansen, Henrik},
month = mar,
year = {2012},
pages = {219--226},
file = {BCR-ABL isoforms associated with intrinsic or acquired resistance to imatinib_ more heterogeneous than just ABL kinase domain point mutations.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/KX28ZDCI/BCR-ABL isoforms associated with intrinsic or acquired resistance to imatinib_ more heterogeneous than just ABL kinase domain point mutations.pdf:application/pdf}
}
@article{Zehir:Nat.Med.:2017,
title = {Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients},
volume = {23},
issn = {1078-8956, 1546-170X},
doi = {10.1038/nm.4333},
timestamp = {2017-08-27T21:17:33Z},
number = {6},
urldate = {2017-08-27},
journal = {Nat. Med.},
author = {Zehir, Ahmet and Benayed, Ryma and Shah, Ronak H and Syed, Aijazuddin and Middha, Sumit and Kim, Hyunjae R and Srinivasan, Preethi and Gao, Jianjiong and Chakravarty, Debyani and Devlin, Sean M and Hellmann, Matthew D and Barron, David A and Schram, Alison M and Hameed, Meera and Dogan, Snjezana and Ross, Dara S and Hechtman, Jaclyn F and DeLair, Deborah F and Yao, JinJuan and Mandelker, Diana L and Cheng, Donavan T and Chandramohan, Raghu and Mohanty, Abhinita S and Ptashkin, Ryan N and Jayakumaran, Gowtham and Prasad, Meera and Syed, Mustafa H and Rema, Anoop Balakrishnan and Liu, Zhen Y and Nafa, Khedoudja and Borsu, Laetitia and Sadowska, Justyna and Casanova, Jacklyn and Bacares, Ruben and Kiecka, Iwona J and Razumova, Anna and Son, Julie B and Stewart, Lisa and Baldi, Tessara and Mullaney, Kerry A and Al-Ahmadie, Hikmat and Vakiani, Efsevia and Abeshouse, Adam A and Penson, Alexander V and Jonsson, Philip and Camacho, Niedzica and Chang, Matthew T and Won, Helen H and Gross, Benjamin E and Kundra, Ritika and Heins, Zachary J and Chen, Hsiao-Wei and Phillips, Sarah and Zhang, Hongxin and Wang, Jiaojiao and Ochoa, Angelica and Wills, Jonathan and Eubank, Michael and Thomas, Stacy B and Gardos, Stuart M and Reales, Dalicia N and Galle, Jesse and Durany, Robert and Cambria, Roy and Abida, Wassim and Cercek, Andrea and Feldman, Darren R and Gounder, Mrinal M and Hakimi, A Ari and Harding, James J and Iyer, Gopa and Janjigian, Yelena Y and Jordan, Emmet J and Kelly, Ciara M and Lowery, Maeve A and Morris, Luc G T and Omuro, Antonio M and Raj, Nitya and Razavi, Pedram and Shoushtari, Alexander N and Shukla, Neerav and Soumerai, Tara E and Varghese, Anna M and Yaeger, Rona and Coleman, Jonathan and Bochner, Bernard and Riely, Gregory J and Saltz, Leonard B and Scher, Howard I and Sabbatini, Paul J and Robson, Mark E and Klimstra, David S and Taylor, Barry S and Baselga, Jose and Schultz, Nikolaus and Hyman, David M and Arcila, Maria E and Solit, David B and Ladanyi, Marc and Berger, Michael F},
month = may,
year = {2017},
pages = {703--713},
file = {nm.4333.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/SDP7AWAI/nm.4333.pdf:application/pdf;nm.4333-S1.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/ZXVCFRWI/nm.4333-S1.pdf:application/pdf}
}
@article{Holohan:Nat.Rev.Cancer:2013,
title = {Cancer Drug Resistance: An Evolving Paradigm},
volume = {13},
issn = {1474-175X, 1474-1768},
shorttitle = {Cancer Drug Resistance},
doi = {10.1038/nrc3599},
timestamp = {2017-08-27T21:32:56Z},
number = {10},
urldate = {2017-08-27},
journal = {Nat. Rev. Cancer},
author = {Holohan, Caitriona and Van Schaeybroeck, Sandra and Longley, Daniel B. and Johnston, Patrick G.},
month = sep,
year = {2013},
pages = {714--726},
file = {nrc3599.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/DVB44KNS/nrc3599.pdf:application/pdf}
}
@article{Nagar:Cell:2003,
title = {Structural Basis for the Autoinhibition of C-{{Abl}} Tyrosine Kinase},
volume = {112},
timestamp = {2017-08-29T19:59:53Z},
number = {6},
urldate = {2017-08-29},
journal = {Cell},
author = {Nagar, Bhushan and Hantschel, Oliver and Young, Matthew A. and Scheffzek, Klaus and Veach, Darren and Bornmann, William and Clarkson, Bayard and Superti-Furga, Giulio and Kuriyan, John},
year = {2003},
pages = {859--871},
file = {1opj_Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/8Q934NX4/1opj_Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase.pdf:application/pdf}
}
@article{Jacobson:ProteinsStruct.Funct.Bioinforma.:2004,
title = {A Hierarchical Approach to All-Atom Protein Loop Prediction},
volume = {55},
issn = {08873585},
doi = {10.1002/prot.10613},
language = {en},
timestamp = {2017-08-29T19:59:59Z},
number = {2},
urldate = {2017-08-29},
journal = {Proteins Struct. Funct. Bioinforma.},
author = {Jacobson, Matthew P. and Pincus, David L. and Rapp, Chaya S. and Day, Tyler J.F. and Honig, Barry and Shaw, David E. and Friesner, Richard A.},
month = mar,
year = {2004},
pages = {351--367},
file = {A hierarchical approach to all-atom protein loop prediction - Jacobson - 2004 - Proteins_ Structure, Function, and Bioinformatics - Wiley Online Library.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/BGZCAB5D/A hierarchical approach to all-atom protein loop prediction - Jacobson - 2004 - Proteins_ Structure, Function, and Bioinformatics - Wiley Online .pdf:application/pdf}
}
@article{Wojcik:J.Biol.Chem.:2016,
title = {Allosteric {{Inhibition}} of {{Bcr}}-{{Abl Kinase}} by {{High Affinity Monobody Inhibitors Directed}} to the {{Src Homology}} 2 ({{SH2}})-{{Kinase Interface}}},
volume = {291},
issn = {0021-9258, 1083-351X},
doi = {10.1074/jbc.M115.707901},
language = {en},
timestamp = {2017-08-29T20:00:02Z},
number = {16},
urldate = {2017-08-29},
journal = {J. Biol. Chem.},
author = {Wojcik, John and Lamontanara, Allan Joaquim and Grabe, Grzegorz and Koide, Akiko and Akin, Louesa and Gerig, Barbara and Hantschel, Oliver and Koide, Shohei},
month = apr,
year = {2016},
pages = {8836--8847},
file = {Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 SH2- Kinase Interface__2016.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/WSACVW92/Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 SH2- Kinase Interface__2016.pdf:application/pdf}
}
@article{Cortes:N.Engl.J.Med.:2013,
title = {A {{Phase}} 2 {{Trial}} of {{Ponatinib}} in {{Philadelphia Chromosome}}\textendash{}{{Positive Leukemias}}},
volume = {369},
issn = {0028-4793, 1533-4406},
doi = {10.1056/NEJMoa1306494},
language = {en},
timestamp = {2017-08-29T20:00:05Z},
number = {19},
urldate = {2017-08-29},
journal = {N. Engl. J. Med.},
author = {Cortes, J.E. and Kim, D.-W. and Pinilla-Ibarz, J. and {le Coutre}, P. and Paquette, R. and Chuah, C. and Nicolini, F.E. and Apperley, J.F. and Khoury, H.J. and Talpaz, M. and DiPersio, J. and DeAngelo, D.J. and Abruzzese, E. and Rea, D. and Baccarani, M. and M{\"u}ller, M.C. and Gambacorti-Passerini, C. and Wong, S. and Lustgarten, S. and Rivera, V.M. and Clackson, T. and Turner, C.D. and Haluska, F.G. and Guilhot, F. and Deininger, M.W. and Hochhaus, A. and Hughes, T. and Goldman, J.M. and Shah, N.P. and Kantarjian, H.},
month = nov,
year = {2013},
pages = {1783--1796},
file = {A Phase 2 Trial of Ponatinib in Philadelphia Chromosome–Positive Leukemias.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/F793RX6I/A Phase 2 Trial of Ponatinib in Philadelphia Chromosome–Positive Leukemias.pdf:application/pdf}
}
@article{Levinson:PLoSBiol.:2006,
title = {A {{Src}}-{{Like Inactive Conformation}} in the {{Abl Tyrosine Kinase Domain}}},
volume = {4},
issn = {1545-7885},
doi = {10.1371/journal.pbio.0040144},
language = {en},
timestamp = {2017-08-29T20:00:08Z},
number = {5},
urldate = {2017-08-29},
journal = {PLoS Biol.},
author = {Levinson, Nicholas M and Kuchment, Olga and Shen, Kui and Young, Matthew A and Koldobskiy, Michael and Karplus, Martin and Cole, Philip A and Kuriyan, John},
editor = {Pawson, Tony},
month = may,
year = {2006},
pages = {e144},
file = {A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain__JohnKuriyan__pH6.5.PDF:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/WVUFVDSB/A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain__JohnKuriyan__pH6.5.PDF:application/pdf}
}
@article{Pemovska:Nature:2015,
title = {Axitinib Effectively Inhibits {{BCR}}-{{ABL1}}({{T315I}}) with a Distinct Binding Conformation},
volume = {519},
issn = {0028-0836, 1476-4687},
doi = {10.1038/nature14119},
timestamp = {2017-08-29T20:00:11Z},
number = {7541},
urldate = {2017-08-29},
journal = {Nature},
author = {Pemovska, Tea and Johnson, Eric and Kontro, Mika and Repasky, Gretchen A. and Chen, Jeffrey and Wells, Peter and Cronin, Ciar{\'a}n N. and McTigue, Michele and Kallioniemi, Olli and Porkka, Kimmo and Murray, Brion W. and Wennerberg, Krister},
month = feb,
year = {2015},
pages = {102--105},
file = {Axitinib effectively inhibits BCR-Abl_T315I with a distinct binding conformation -- Pemovska et al. -- Nature -- 2015.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/6R3AKR6V/Axitinib effectively inhibits BCR-Abl_T315I with a distinct binding conformation -- Pemovska et al. -- Nature -- 2015.pdf:application/pdf}
}
@article{Littlefield:Chem.Biol.:2014,
title = {{{RETRACTED}}: {{An ATP}}-{{Competitive Inhibitor Modulates}} the {{Allosteric Function}} of the {{HER3 Pseudokinase}}},
volume = {21},
issn = {10745521},
shorttitle = {{{RETRACTED}}},
doi = {10.1016/j.chembiol.2014.02.011},
language = {en},
timestamp = {2017-08-29T20:00:17Z},
number = {4},
urldate = {2017-08-29},
journal = {Chem. Biol.},
author = {Littlefield, Peter and Moasser, Mark~M. and Jura, Natalia},
month = apr,
year = {2014},
pages = {453--458},
file = {bosutinib_HER3,Abl,CamKII__nihms570362.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/4E3H5TV2/bosutinib_HER3,Abl,CamKII__nihms570362.pdf:application/pdf}
}
@article{McClendon:Proc.Natl.Acad.Sci.:2014,
title = {Dynamic Architecture of a Protein Kinase},
volume = {111},
issn = {0027-8424, 1091-6490},
doi = {10.1073/pnas.1418402111},
language = {en},
timestamp = {2017-08-29T20:00:26Z},
number = {43},
urldate = {2017-08-29},
journal = {Proc. Natl. Acad. Sci.},
author = {McClendon, C. L. and Kornev, A. P. and Gilson, M. K. and Taylor, S. S.},
month = oct,
year = {2014},
pages = {E4623--E4631},
file = {Dynamic architecture of a protein kinase.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/JQIS7JAD/Dynamic architecture of a protein kinase.pdf:application/pdf}
}
@article{Seeliger:CancerRes.:2009,
title = {Equally {{Potent Inhibition}} of C-{{Src}} and {{Abl}} by {{Compounds}} That {{Recognize Inactive Kinase Conformations}}},
volume = {69},
issn = {0008-5472, 1538-7445},
doi = {10.1158/0008-5472.CAN-08-3953},
language = {en},
timestamp = {2017-08-29T20:00:29Z},
number = {6},
urldate = {2017-08-29},
journal = {Cancer Res.},
author = {Seeliger, M. A. and Ranjitkar, P. and Kasap, C. and Shan, Y. and Shaw, D. E. and Shah, N. P. and Kuriyan, J. and Maly, D. J.},
month = mar,
year = {2009},
pages = {2384--2392},
file = {Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/V4Q53P7J/Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations.pdf:application/pdf}
}
@article{Zhao:ACSChem.Biol.:2014,
title = {Exploration of {{Type II Binding Mode}}: {{A Privileged Approach}} for {{Kinase Inhibitor Focused Drug Discovery}}?},
volume = {9},
issn = {1554-8929, 1554-8937},
shorttitle = {Exploration of {{Type II Binding Mode}}},
doi = {10.1021/cb500129t},
language = {en},
timestamp = {2017-08-29T20:00:32Z},
number = {6},
urldate = {2017-08-29},
journal = {ACS Chem. Biol.},
author = {Zhao, Zheng and Wu, Hong and Wang, Li and Liu, Yi and Knapp, Stefan and Liu, Qingsong and Gray, Nathanael S.},
month = jun,
year = {2014},
pages = {1230--1241},
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volume = {3},
issn = {1549-9618, 1549-9626},
shorttitle = {Improved {{Methods}} for {{Side Chain}} and {{Loop Predictions}} via the {{Protein Local Optimization Program}}},
doi = {10.1021/ct700166f},
language = {en},
timestamp = {2017-08-29T20:00:35Z},
number = {6},
urldate = {2017-08-29},
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year = {2007},
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@book{::2016,
address = {New York, NY},
title = {Boundaryless Hospital: Rethink and Redefine Health Care Management},
isbn = {978-3-662-49010-5},
shorttitle = {Boundaryless Hospital},
timestamp = {2017-08-29T20:00:41Z},
publisher = {{Springer Berlin Heidelberg}},
year = {2016},
file = {Personalized Medicine Challenges the Health Care System _ SpringerLink.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/TUZ2TAAH/Personalized Medicine Challenges the Health Care System _ SpringerLink.pdf:application/pdf}
}
@article{Cortes:N.Engl.J.Med.:2012,
title = {Ponatinib in {{Refractory Philadelphia Chromosome}}\textendash{}{{Positive Leukemias}}},
volume = {367},
issn = {0028-4793, 1533-4406},
doi = {10.1056/NEJMoa1205127},
language = {en},
timestamp = {2017-08-29T20:00:44Z},
number = {22},
urldate = {2017-08-29},
journal = {N. Engl. J. Med.},
author = {Cortes, Jorge E. and Kantarjian, Hagop and Shah, Neil P. and Bixby, Dale and Mauro, Michael J. and Flinn, Ian and O'Hare, Thomas and Hu, Simin and Narasimhan, Narayana I. and Rivera, Victor M. and Clackson, Tim and Turner, Christopher D. and Haluska, Frank G. and Druker, Brian J. and Deininger, Michael W.N. and Talpaz, Moshe},
month = nov,
year = {2012},
pages = {2075--2088},
file = {Ponatinib in Refractory Philadelphia Chromosome–Positive Leukemias.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/T57S2K3R/Ponatinib in Refractory Philadelphia Chromosome–Positive Leukemias.pdf:application/pdf}
}
@article{Zhou:Chem.Biol.DrugDes.:2011,
title = {Structural {{Mechanism}} of the {{Pan}}-{{BCR}}-{{ABL Inhibitor Ponatinib}} ({{AP24534}}): {{Lessons}} for {{Overcoming Kinase Inhibitor Resistance}}: {{Structural Mechanism}} of {{Ponatinib}}},
volume = {77},
issn = {17470277},
shorttitle = {Structural {{Mechanism}} of the {{Pan}}-{{BCR}}-{{ABL Inhibitor Ponatinib}} ({{AP24534}})},
doi = {10.1111/j.1747-0285.2010.01054.x},
language = {en},
timestamp = {2017-08-29T20:00:47Z},
number = {1},
urldate = {2017-08-29},
journal = {Chem. Biol. Drug Des.},
author = {Zhou, Tianjun and Commodore, Lois and Huang, Wei-Sheng and Wang, Yihan and Thomas, Mathew and Keats, Jeff and Xu, Qihong and Rivera, Victor M. and Shakespeare, William C. and Clackson, Tim and Dalgarno, David C. and Zhu, Xiaotian},
month = jan,
year = {2011},
pages = {1--11},
file = {Ponatinib--Structural mechanism of the Pan-BCR-ABl inhibitor Ponatiinb-- Lessons--CBDD--2011.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/JZMX372N/Ponatinib--Structural mechanism of the Pan-BCR-ABl inhibitor Ponatiinb-- Lessons--CBDD--2011.pdf:application/pdf}
}
@article{Prasad:LancetOncol.:2016,
title = {Precision Oncology: Origins, Optimism, and Potential},
volume = {17},
issn = {14702045},
shorttitle = {Precision Oncology},
doi = {10.1016/S1470-2045(15)00620-8},
language = {en},
timestamp = {2017-08-29T20:00:50Z},
number = {2},
urldate = {2017-08-29},
journal = {Lancet Oncol.},
author = {Prasad, Vinay and Fojo, Tito and Brada, Michael},
month = feb,
year = {2016},
pages = {e81--e86},
file = {Precision oncology_ origins, optimism, and potential - ScienceDirect.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/WXWZH8EM/Precision oncology_ origins, optimism, and potential - ScienceDirect.pdf:application/pdf}
}
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title = {Predicting the {{Effect}} of {{Amino Acid Single}}-{{Point Mutations}} on {{Protein Stability}}\textemdash{}{{Large}}-{{Scale Validation}} of {{MD}}-{{Based Relative Free Energy Calculations}}},
volume = {429},
issn = {00222836},
doi = {10.1016/j.jmb.2016.12.007},
language = {en},
timestamp = {2017-08-29T20:00:53Z},
number = {7},
urldate = {2017-08-29},
journal = {J. Mol. Biol.},
author = {Steinbrecher, Thomas and Zhu, Chongkai and Wang, Lingle and Abel, Robert and Negron, Christopher and Pearlman, David and Feyfant, Eric and Duan, Jianxin and Sherman, Woody},
month = apr,
year = {2017},
pages = {948--963},
file = {Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/SXCD4QGE/Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calcula.pdf:application/pdf}
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@article{Dolker:PLoSComput.Biol.:2014,
title = {The {{SH2 Domain Regulates}} C-{{Abl Kinase Activation}} by a {{Cyclin}}-{{Like Mechanism}} and {{Remodulation}} of the {{Hinge Motion}}},
volume = {10},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1003863},
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author = {D{\"o}lker, Nicole and G{\'o}rna, Maria W. and Sutto, Ludovico and Torralba, Antonio S. and Superti-Furga, Giulio and Gervasio, Francesco L.},
editor = {Wei, Guanghong},
month = oct,
year = {2014},
pages = {e1003863},
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@article{Sellers:ProteinsStruct.Funct.Bioinforma.:2008,
title = {Toward Better Refinement of Comparative Models: {{Predicting}} Loops in Inexact Environments},
volume = {72},
issn = {08873585},
shorttitle = {Toward Better Refinement of Comparative Models},
doi = {10.1002/prot.21990},
language = {en},
timestamp = {2017-08-29T20:01:08Z},
number = {3},
urldate = {2017-08-29},
journal = {Proteins Struct. Funct. Bioinforma.},
author = {Sellers, Benjamin D. and Zhu, Kai and Zhao, Suwen and Friesner, Richard A. and Jacobson, Matthew P.},
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@article{Gozgit3992,
title = {Comprehensive {{Analysis Of The In Vitro Potency Of Ponatinib}}, and {{All Other Approved BCR}}-{{ABL Tyrosine Kinase Inhibitors}} ({{TKIs}}), {{Against}} a {{Panel Of Single}} and {{Compound BCR}}-{{ABL Mutants}}},
volume = {122},
issn = {0006-4971},
abstract = {Background Secondary mutations in BCR-ABL are the most common cause of resistance to TKIs in patients (pts) with chronic myeloid leukemia (CML). Ponatinib is a potent pan-BCR-ABL TKI that has been shown to suppress the emergence of any single mutation in vitro, including T315I, at clinically achievable concentrations (40 nM), though higher concentrations were required to suppress emergence of certain compound mutations (2 mutations in the same BCR-ABL allele). Ponatinib has demonstrated significant clinical activity in pts in the phase 2 PACE trial, 60\% of whom received 3 or more prior TKIs. Responses were observed for each of the 15 mutations present in \>1 chronic phase CML pt at baseline, and no single mutation conferring resistance to ponatinib has emerged to date, though in some cases development of compound mutations has been observed. To gain a more precise understanding of the effects of specific mutations on the clinical efficacy of ponatinib, IC50s for ponatinib, and all other approved TKIs, against 31 single or compound BCR-ABL mutants were determined. To explore the relationship between in vitro potency and clinical efficacy, IC50s were related to ``effective'' TKI levels achieved in patients.Methods TKI potency was assessed in engineered Ba/F3 cells by measuring cell viability at 72 hours. The effective plasma concentration for each TKI was calculated from published average steady-state concentration values for the recommended dose, and adjusted for the functional effects of protein binding. These effects were assessed by determining the degree to which TKI potency was reduced by the presence of physiological concentrations of human serum albumin (HSA) and alpha 1-acid glycoprotein (AAG).Results The activity of ponatinib, and 5 other TKIs, against 21 single BCR-ABL mutants is shown in Figure A. Ponatinib potently inhibited viability of native BCR-ABL and all mutants, including T315I (IC50s (nM): 3-16). The IC50s for the other TKIs, excluding T315I (\>4000 for all) ranged from: 201-10,000 (imatinib), 12-784 (nilotinib), 2-104 (dasatinib), 40-1,280 (bosutinib) and 18-5,216 (radotinib). IC50 values were compared to the effective plasma concentration for each TKI (Figure A). Mutants that have previously been associated with clinical resistance to a particular TKI tended to have IC50s that approached or substantially exceeded the effective concentration for that TKI, including most mutants for imatinib, E255K/V, Y253H, L248R, T315I for nilotinib, and V299L, F317C/I/V, T315A/I for dasatinib. The most problematic mutants for bosutinib predicted by this analysis were F317V, L248R, V299L, and T315I. Notably, all mutant IC50s fell below the effective concentration for ponatinib. The activity of all TKIs against 10 clinically-observed BCR-ABL compound mutants was also assessed. Four compound mutants had IC50s near or above the effective concentration for ponatinib (T315I+M351T, E255V+F317I, T315I+E255K, T315I+E255V) (Figure B). All 4, plus others, are also predicted to be problematic for the other TKIs.Conclusions Relating in vitro TKI potency to ``effective'' steady-state plasma concentrations in patients identified mutations known to confer clinical resistance to imatinib, nilotinib and dasatinib. This method of analysis suggests that ponatinib may be able to inhibit all single BCR-ABL mutants, but not all compound mutants, a prediction that is thus far consistent with results observed in patients. Compound mutations that are predicted to confer resistance to ponatinib are also predicted to confer resistance to all other approved TKIs. Early introduction of ponatinib may prevent the emergence of single mutations, and thus the sequential development of compound mutations.Disclosures: Gozgit: ARIAD: Employment, Equity Ownership. Schrock: ARIAD: Employment, Equity Ownership. Chen: ARIAD: Employment, Equity Ownership. Clackson: ARIAD: employees of and own stock/stock options in ARIAD Pharmaceuticals, Inc Other, Employment. Rivera: ARIAD: Employment.$\carriagereturn$* Asterisk with author names denotes non-ASH members.},
timestamp = {2017-08-29T21:08:11Z},
number = {21},
journal = {Blood},
author = {Schrock, Alexa and Chen, Tzu-Hsiu and Clackson, Tim and Rivera, Victor M.},
editor = {Gozgit, Joseph M},
year = {2013},
pages = {3992--3992}
}
@article{doi:10.1200/PO.17.00011,
title = {{{OncoKB}}: {{A Precision Oncology Knowledge Base}}},
doi = {10.1200/PO.17.00011},
abstract = {PurposeWith prospective clinical sequencing of tumors emerging as a mainstay in cancer care, an urgent need exists for a clinical support tool that distills the clinical implications associated with specific mutation events into a standardized and easily interpretable format. To this end, we developed OncoKB, an expert-guided precision oncology knowledge base.MethodsOncoKB annotates the biologic and oncogenic effects and prognostic and predictive significance of somatic molecular alterations. Potential treatment implications are stratified by the level of evidence that a specific molecular alteration is predictive of drug response on the basis of US Food and Drug Administration labeling, National Comprehensive Cancer Network guidelines, disease-focused expert group recommendations, and scientific literature.ResultsTo date, $>$ 3,000 unique mutations, fusions, and copy number alterations in 418 cancer-associated genes have been annotated. To test the utility of OncoKB, we annotated all genomic events in 5,983 primary tumor samples in 19 cancer types. Forty-one percent of samples harbored at least one potentially actionable alteration, of which 7.5\% were predictive of clinical benefit from a standard treatment. OncoKB annotations are available through a public Web resource (http://oncokb.org) and are incorporated into the cBioPortal for Cancer Genomics to facilitate the interpretation of genomic alterations by physicians and researchers.ConclusionOncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions.},
timestamp = {2017-08-29T21:43:57Z},
number = {1},
journal = {JCO Precis. Oncol.},
author = {Chakravarty, Debyani and Gao, Jianjiong and Phillips, Sarah and Kundra, Ritika and Zhang, Hongxin and Wang, Jiaojiao and Rudolph, Julia E. and Yaeger, Rona and Soumerai, Tara and Nissan, Moriah H. and Chang, Matthew T. and Chandarlapaty, Sarat and Traina, Tiffany A. and Paik, Paul K. and Ho, Alan L. and Hantash, Feras M. and Grupe, Andrew and Baxi, Shrujal S. and Callahan, Margaret K. and Snyder, Alexandra and Chi, Ping and Danila, Daniel C. and Gounder, Mrinal and Harding, James J. and Hellmann, Matthew D. and Iyer, Gopa and Janjigian, Yelena Y. and Kaley, Thomas and Levine, Douglas A. and Lowery, Maeve and Omuro, Antonio and Postow, Michael A. and Rathkopf, Dana and Shoushtari, Alexander N. and Shukla, Neerav and Voss, Martin H. and Paraiso, Ederlinda and Zehir, Ahmet and Berger, Michael F. and Taylor, Barry S. and Saltz, Leonard B. and Riely, Gregory J. and Ladanyi, Marc and Hyman, David M. and Baselga, Jos{\'e} and Sabbatini, Paul and Solit, David B. and Schultz, Nikolaus},
year = {2017},
pages = {1--16},
file = {po.17.00011.pdf:/Users/choderaj/Library/Application Support/Zotero/Profiles/ydy6bajg.default/zotero/storage/RAZKVC7M/po.17.00011.pdf:application/pdf}
}
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volume = {137},
issn = {0002-7863, 1520-5126},
doi = {10.1021/ja512751q},
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month = feb,
year = {2015},
pages = {2695--2703},
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}
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title = {Accurate Calculation of the Absolute Free Energy of Binding for Drug Molecules},
volume = {7},
issn = {2041-6520, 2041-6539},
doi = {10.1039/C5SC02678D},
language = {en},
timestamp = {2017-08-29T22:03:10Z},
number = {1},
urldate = {2017-08-29},
journal = {Chem Sci},
author = {Aldeghi, Matteo and Heifetz, Alexander and Bodkin, Michael J. and Knapp, Stefan and Biggin, Philip C.},
year = {2016},
pages = {207--218},
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volume = {138},
issn = {0002-7863, 1520-5126},
shorttitle = {Experimental and {{Computational Analysis}} of {{Protein Stabilization}} by {{Gly}}-to- $<$span Style="font-Variant},
doi = {10.1021/jacs.6b09511},
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issn = {00064971, 15280020},
doi = {10.1182/blood.V99.9.3472},
timestamp = {2017-08-30T21:13:29Z},
number = {9},
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author = {Branford, S.},
month = may,
year = {2002},
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}
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title = {Fighting Cancer Drug Resistance: {{Opportunities}} and Challenges for Mutation-Specific {{EGFR}} Inhibitors},
volume = {20},
issn = {13687646},
shorttitle = {Fighting Cancer Drug Resistance},
doi = {10.1016/j.drup.2015.05.002},
language = {en},
timestamp = {2017-08-30T21:15:00Z},
urldate = {2017-08-30},
journal = {Drug Resist. Updat.},
author = {Juchum, Michael and G{\"u}nther, Marcel and Laufer, Stefan A.},
month = may,
year = {2015},
pages = {12--28},
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doi = {10.1016/j.apsb.2014.12.007},
language = {en},
timestamp = {2017-08-30T21:15:39Z},
number = {1},
urldate = {2017-08-30},
journal = {Acta Pharm. Sin. B},
author = {Song, Zilan and Wang, Meining and Zhang, Ao},
month = jan,
year = {2015},
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}
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title = {Targeting the Cancer Kinome through Polypharmacology},
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timestamp = {2017-08-30T21:16:26Z},
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}
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title = {Comprehensive Mutational Scanning of a Kinase {\emph{in Vivo}} Reveals Substrate-Dependent Fitness Landscapes},
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issn = {0305-1048, 1362-4962},
doi = {10.1093/nar/gku511},
language = {en},
timestamp = {2017-08-30T21:18:01Z},
number = {14},
urldate = {2017-08-30},
journal = {Nucleic Acids Res.},
author = {Melnikov, Alexandre and Rogov, Peter and Wang, Li and Gnirke, Andreas and Mikkelsen, Tarjei S.},
month = aug,
year = {2014},
pages = {e112--e112},
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}
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doi = {10.1063/1.4769292},
language = {en},
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shorttitle = {{{OPLS3}}},
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