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\begin{thebibliography}{241}
\providecommand{\natexlab}[1]{#1}
\providecommand{\urlprefix}{}
\providecommand{\doiprefix}{doi: }
\bibitem[{Siegel et~al.(2018)Siegel, Rebecca L and Miller, Kimberly D and
Jemal, Ahmedin}]{Siegel:2018cq}
\textbf{\color{eLifeMediumGrey} Siegel RL}, Miller KD, Jemal A.
\newblock {Cancer statistics, 2018.}
\newblock CA: a cancer journal for clinicians. 2018 Jan; 68(1):7--30.
\bibitem[{Cohen and Tcherpakov(2010{\natexlab{a}})Cohen, Philip and Tcherpakov,
Marianna}]{Cohen:2010fs}
\textbf{\color{eLifeMediumGrey} Cohen P}, Tcherpakov M.
\newblock {Will the ubiquitin system furnish as many drug targets as protein
kinases?}
\newblock Cell. 2010 Nov; 143(5):686--693.
\bibitem[{{Robert Roskoski Jr}(2017)}]{fda-approved-kinase-inhibitors}
\textbf{\color{eLifeMediumGrey} {Robert Roskoski Jr}}.
\newblock {{USFDA}} Approved Protein Kinase Inhibitors.
\newblock . 2017; \urlprefix\url{http://www.brimr.org/PKI/PKIs.htm}, updated 3
May 2017.
\bibitem[{{Paul, Steven M} et~al.(2010){Paul, Steven M} and {Mytelka, Daniel S}
and {Dunwiddie, Christopher T} and {Persinger, Charles C} and {Munos, Bernard
H} and {Lindborg, Stacy R} and {Schacht, Aaron L}}]{Paul:2010ff}
\textbf{\color{eLifeMediumGrey} {Paul, Steven M}}, {Mytelka, Daniel S},
{Dunwiddie, Christopher T}, {Persinger, Charles C}, {Munos, Bernard H},
{Lindborg, Stacy R}, {Schacht, Aaron L}.
\newblock {How to improve R{\&}D productivity: the pharmaceutical industry's
grand challenge.}
\newblock Nature reviews Drug discovery. 2010 Mar; 9(3):203--214.
\bibitem[{Sanchez-Vega et~al.(2018)Sanchez-Vega, Francisco and Hechtman, Jaclyn
F and Castel, Pau and Ku, Geoffrey Y and Tuvy, Yaelle and Won, Helen and
Fong, Christoper J and Bouvier, Nancy and Nanjangud, Gouri J and Soong,
Joanne and Vakiani, Efsevia and Schattner, Mark and Kelsen, David P and
Lefkowitz, Robert A and Brown, Karen and Lacouture, Mario E and Capanu,
Marinela and Mattar, Marissa and Qeriqi, Besnik and Cecchi, Fabiola and Tian,
Yuan and Hembrough, Todd and Nagy, Rebecca J and Lanman, Richard B and
Larson, Steven M and Pandit-Taskar, Neeta and Schoder, Heiko and
Iacobuzio-Donahue, Christine A and Ilson, David H and Weber, Wolfgang A and
Berger, Michael F and de Stanchina, Elisa and Taylor, Barry S and Lewis,
Jason S and Solit, David B and Carrasquillo, Jorge A and Scaltriti, Maurizio
and Schultz, Nikolaus and Janjigian, Yelena Y}]{SanchezVega:2018jg}
\textbf{\color{eLifeMediumGrey} Sanchez-Vega F}, Hechtman JF, Castel P, Ku GY,
Tuvy Y, Won H, Fong CJ, Bouvier N, Nanjangud GJ, Soong J, Vakiani E,
Schattner M, Kelsen DP, Lefkowitz RA, Brown K, Lacouture ME, Capanu M, Mattar
M, Qeriqi B, Cecchi F, et~al.
\newblock {EGFR and MET Amplifications Determine Response to HER2 Inhibition in
ERBB2-Amplified Esophagogastric Cancer.}
\newblock Cancer discovery. 2018 Nov; .
\bibitem[{Bose et~al.(2013)Bose, Ron and Kavuri, Shyam M and Searleman, Adam C
and Shen, Wei and Shen, Dong and Koboldt, Daniel C and Monsey, John and Goel,
Nicholas and Aronson, Adam B and Li, Shunqiang and Ma, Cynthia X and Ding, Li
and Mardis, Elaine R and Ellis, Matthew J}]{Bose:2013gl}
\textbf{\color{eLifeMediumGrey} Bose R}, Kavuri SM, Searleman AC, Shen W, Shen
D, Koboldt DC, Monsey J, Goel N, Aronson AB, Li S, Ma CX, Ding L, Mardis ER,
Ellis MJ.
\newblock {Activating HER2 mutations in HER2 gene amplification negative breast
cancer.}
\newblock Cancer discovery. 2013 Feb; 3(2):224--237.
\bibitem[{Prahallad et~al.(2012)Prahallad, Anirudh and Sun, Chong and Huang,
Sidong and Di Nicolantonio, Federica and Salazar, Ramon and Zecchin, Davide
and Beijersbergen, Roderick L and Bardelli, Alberto and Bernards,
Ren{\'e}}]{Prahallad:2012iw}
\textbf{\color{eLifeMediumGrey} Prahallad A}, Sun C, Huang S, Di~Nicolantonio
F, Salazar R, Zecchin D, Beijersbergen RL, Bardelli A, Bernards R.
\newblock {Unresponsiveness of colon cancer to BRAF(V600E) inhibition through
feedback activation of EGFR.}
\newblock Nature. 2012 Mar; 483(7387):100--103.
\bibitem[{Engelman et~al.(2007)Engelman, Jeffrey A and Zejnullahu, Kreshnik and
Mitsudomi, Tetsuya and Song, Youngchul and Hyland, Courtney and Park, Joon Oh
and Lindeman, Neal and Gale, Christopher-Michael and Zhao, Xiaojun and
Christensen, James and Kosaka, Takayuki and Holmes, Alison J and Rogers,
Andrew M and Cappuzzo, Federico and Mok, Tony and Lee, Charles and Johnson,
Bruce E and Cantley, Lewis C and J{\"a}nne, Pasi A}]{Engelman:2007ka}
\textbf{\color{eLifeMediumGrey} Engelman JA}, Zejnullahu K, Mitsudomi T, Song
Y, Hyland C, Park JO, Lindeman N, Gale CM, Zhao X, Christensen J, Kosaka T,
Holmes AJ, Rogers AM, Cappuzzo F, Mok T, Lee C, Johnson BE, Cantley LC,
J{\"a}nne PA.
\newblock {MET amplification leads to gefitinib resistance in lung cancer by
activating ERBB3 signaling.}
\newblock Science. 2007 May; 316(5827):1039--1043.
\bibitem[{Pao et~al.(2005)Pao, William and Miller, Vincent A and Politi,
Katerina A and Riely, Gregory J and Somwar, Romel and Zakowski, Maureen F nd
Kris, Mark G and Varmus, Harold}]{Pao:2005dp}
\textbf{\color{eLifeMediumGrey} Pao W}, Miller VA, Politi KA, Riely GJ, Somwar
R, Zakowski MG Maureen F nd~Kris, Varmus H.
\newblock {Acquired resistance of lung adenocarcinomas to gefitinib or
erlotinib is associated with a second mutation in the EGFR kinase domain.}
\newblock PLoS medicine. 2005 Mar; 2(3):e73.
\bibitem[{Drilon et~al.(2017)Drilon, Alexander and Nagasubramanian, Ramamoorthy
and Blake, James F and Ku, Nora and Tuch, Brian B and Ebata, Kevin and Smith,
Steve and Lauriault, Veronique and Kolakowski, Gabrielle R and Brandhuber,
Barbara J and Larsen, Paul D and Bouhana, Karyn S and Winski, Shannon L and
Hamor, Robyn and Wu, Wen-I and Parker, Andrew and Morales, Tony H and
Sullivan, Francis X and DeWolf, Walter E and Wollenberg, Lance A and Gordon,
Paul R and Douglas-Lindsay, Dorothea N and Scaltriti, Maurizio and Benayed,
Ryma and Raj, Sandeep and Hanusch, Bethany and Schram, Alison M and Jonsson,
Philip and Berger, Michael F and Hechtman, Jaclyn F and Taylor, Barry S and
Andrews, Steve and Rothenberg, S Michael and Hyman, David M}]{Drilon:2017gb}
\textbf{\color{eLifeMediumGrey} Drilon A}, Nagasubramanian R, Blake JF, Ku N,
Tuch BB, Ebata K, Smith S, Lauriault V, Kolakowski GR, Brandhuber BJ, Larsen
PD, Bouhana KS, Winski SL, Hamor R, Wu WI, Parker A, Morales TH, Sullivan FX,
DeWolf WE, Wollenberg LA, et~al.
\newblock {A Next-Generation TRK Kinase Inhibitor Overcomes Acquired Resistance
to Prior TRK Kinase Inhibition in Patients with TRK Fusion-Positive Solid
Tumors.}
\newblock Cancer discovery. 2017 Sep; 7(9):963--972.
\bibitem[{Knight et~al.(2010{\natexlab{a}})Knight, Zachary A. and Lin, Henry
and Shokat, Kevan M.}]{Knight:Nat.Rev.Cancer:2010}
\textbf{\color{eLifeMediumGrey} Knight ZA}, Lin H, Shokat KM.
\newblock Targeting the Cancer Kinome through Polypharmacology.
\newblock Nat Rev Cancer. 2010; 10(2):130.
\bibitem[{Chandarlapaty et~al.(2011{\natexlab{a}})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}]{Chandarlapaty:CancerCell:2011}
\textbf{\color{eLifeMediumGrey} Chandarlapaty S}, Sawai A, Scaltriti M,
Rodrik-Outmezguine V, Grbovic-Huezo O, Serra V, Majumder PK, Baselga J, Rosen
N.
\newblock {{AKT Inhibition Relieves Feedback Suppression}} of {{Receptor
Tyrosine Kinase Expression}} and {{Activity}}.
\newblock Cancer Cell. 2011 Jan; 19(1):58--71.
\newblock \href{10.1016/j.ccr.2010.10.031}{\doiprefix
\detokenize{10.1016/j.ccr.2010.10.031}}.
\bibitem[{Rudmann(2013)Rudmann, Daniel G}]{Rudmann2013-hi}
\textbf{\color{eLifeMediumGrey} Rudmann DG}.
\newblock On-target and off-target-based toxicologic effects.
\newblock Toxicol Pathol. 2013 Feb; 41(2):310--314.
\bibitem[{Liu and Kurzrock(2014)Liu, Sariah and Kurzrock, Razelle}]{Liu2014-yi}
\textbf{\color{eLifeMediumGrey} Liu S}, Kurzrock R.
\newblock Toxicity of targeted therapy: Implications for response and impact of
genetic polymorphisms.
\newblock Cancer Treat Rev. 2014 Aug; 40(7):883--891.
\bibitem[{Manning et~al.(2002{\natexlab{a}})Manning, G and Whyte, D B and
Martinez, R and Hunter, T and Sudarsanam, S}]{Manning2002-cw}
\textbf{\color{eLifeMediumGrey} Manning G}, Whyte DB, Martinez R, Hunter T,
Sudarsanam S.
\newblock The Protein Kinase Complement of the Human Genome.
\newblock Science. 2002 Dec; 298(5600):1912--1934.
\bibitem[{Cowan-Jacob et~al.(2007)Cowan-Jacob, S W and Fendrich, G and
Floersheimer, A and Furet, P and Liebetanz, J and Rummel, G and Rheinberger,
P and Centeleghe, M and Fabbro, D and Manley, P W and
{IUCr}}]{Cowan-Jacob2007-rn}
\textbf{\color{eLifeMediumGrey} Cowan-Jacob SW}, Fendrich G, Floersheimer A,
Furet P, Liebetanz J, Rummel G, Rheinberger P, Centeleghe M, Fabbro D, Manley
PW, {IUCr}.
\newblock Structural biology contributions to the discovery of drugs to treat
chronic myelogenous leukaemia.
\newblock Acta Crystallogr D Biol Crystallogr. 2007 Jan; 63(1):80--93.
\bibitem[{Seeliger et~al.(2007)Seeliger, Markus A and Nagar, Bhushan and Frank,
Filipp and Cao, Xiaoxian and Henderson, M Nidanie and Kuriyan,
John}]{Seeliger2007-jn}
\textbf{\color{eLifeMediumGrey} Seeliger MA}, Nagar B, Frank F, Cao X,
Henderson MN, Kuriyan J.
\newblock c-Src Binds to the Cancer Drug Imatinib with an Inactive {Abl/c-Kit}
Conformation and a Distributed Thermodynamic Penalty.
\newblock Structure. 2007 Mar; 15(3):299--311.
\bibitem[{Huse and Kuriyan(2002)Huse, M and Kuriyan, J}]{Huse2002-ml}
\textbf{\color{eLifeMediumGrey} Huse M}, Kuriyan J.
\newblock The conformational plasticity of protein kinases.
\newblock Cell. 2002 Jan; 109(3):275--282.
\bibitem[{Harrison(2003)Harrison, Stephen C}]{Harrison2003-ct}
\textbf{\color{eLifeMediumGrey} Harrison SC}.
\newblock Variation on an Src-like theme.
\newblock Cell. 2003 Mar; 112(6):737--740.
\bibitem[{Nagar et~al.(2003{\natexlab{a}})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}]{Nagar:2003tu}
\textbf{\color{eLifeMediumGrey} Nagar B}, Hantschel O, Young MA, Scheffzek K,
Veach D, Bornmann W, Clarkson B, Superti-Furga G, Kuriyan J.
\newblock {Structural basis for the autoinhibition of c-Abl tyrosine kinase.}
\newblock Cell. 2003 Mar; 112(6):859--871.
\bibitem[{Davis et~al.(2011{\natexlab{a}})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}]{Davis:Nat.Biotechnol.:2011}
\textbf{\color{eLifeMediumGrey} Davis MI}, Hunt JP, Herrgard S, Ciceri P,
Wodicka LM, Pallares G, Hocker M, Treiber DK, Zarrinkar PP.
\newblock Comprehensive Analysis of Kinase Inhibitor Selectivity.
\newblock Nat Biotechnol. 2011 Oct; 29(11):1046--1051.
\newblock \href{10.1038/nbt.1990}{\doiprefix \detokenize{10.1038/nbt.1990}}.
\bibitem[{Apsel et~al.(2008)Apsel, Beth and Blair, Jimmy A and Gonzalez,
Beatriz and Nazif, Tamim M and Feldman, Morri E and Aizenstein, Brian and
Hoffman, Randy and Williams, Roger L and Shokat, Kevan M and Knight, Zachary
A}]{Apsel2008-it}
\textbf{\color{eLifeMediumGrey} Apsel B}, Blair JA, Gonzalez B, Nazif TM,
Feldman ME, Aizenstein B, Hoffman R, Williams RL, Shokat KM, Knight ZA.
\newblock Targeted polypharmacology: discovery of dual inhibitors of tyrosine
and phosphoinositide kinases.
\newblock Nat Chem Biol. 2008 Nov; 4(11):691--699.
\bibitem[{Hopkins et~al.(2006)Hopkins, Andrew L and Mason, Jonathan S and
Overington, John P}]{Hopkins2006-qu}
\textbf{\color{eLifeMediumGrey} Hopkins AL}, Mason JS, Overington JP.
\newblock Can we rationally design promiscuous drugs?
\newblock Curr Opin Struct Biol. 2006 Feb; 16(1):127--136.
\bibitem[{Hopkins(2008)Hopkins, Andrew L}]{Hopkins2008-ij}
\textbf{\color{eLifeMediumGrey} Hopkins AL}.
\newblock Network pharmacology: the next paradigm in drug discovery.
\newblock Nat Chem Biol. 2008 Nov; 4(11):682--690.
\bibitem[{Zhang et~al.(2009)Zhang, Jianming and Yang, Priscilla L and Gray,
Nathanael S}]{Zhang2009-il}
\textbf{\color{eLifeMediumGrey} Zhang J}, Yang PL, Gray NS.
\newblock Targeting cancer with small molecule kinase inhibitors.
\newblock Nat Rev Cancer. 2009 Jan; 9(1):28--39.
\bibitem[{Huggins et~al.(2012)Huggins, David J and Sherman, Woody and Tidor,
Bruce}]{Huggins2012-hr}
\textbf{\color{eLifeMediumGrey} Huggins DJ}, Sherman W, Tidor B.
\newblock Rational approaches to improving selectivity in drug design.
\newblock J Med Chem. 2012 Feb; 55(4):1424--1444.
\bibitem[{Mendoza et~al.(2011)Mendoza, Michelle C and Er, E Emrah and Blenis,
John}]{Mendoza2011-bj}
\textbf{\color{eLifeMediumGrey} Mendoza MC}, Er EE, Blenis J.
\newblock The {Ras-ERK} and {PI3K-mTOR} pathways: cross-talk and compensation.
\newblock Trends Biochem Sci. 2011 Jun; 36(6):320--328.
\bibitem[{Tricker et~al.(2015)Tricker, Erin M and Xu, Chunxiao and Uddin,
Sharmeen and Capelletti, Marzia and Ercan, Dalia and Ogino, Atsuko and
Pratilas, Christine A and Rosen, Neal and Gray, Nathanael S and Wong,
Kwok-Kin and J{\"a}nne, Pasi A}]{Tricker2015-xx}
\textbf{\color{eLifeMediumGrey} Tricker EM}, Xu C, Uddin S, Capelletti M, Ercan
D, Ogino A, Pratilas CA, Rosen N, Gray NS, Wong KK, J{\"a}nne PA.
\newblock Combined {EGFR/MEK} Inhibition Prevents the Emergence of Resistance
in {EGFR-Mutant} Lung Cancer.
\newblock Cancer Discov. 2015 Sep; 5(9):960--971.
\bibitem[{Chandarlapaty et~al.(2011{\natexlab{b}})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,
Jos{\'e} and Rosen, Neal}]{Chandarlapaty2011-cq}
\textbf{\color{eLifeMediumGrey} Chandarlapaty S}, Sawai A, Scaltriti M,
Rodrik-Outmezguine V, Grbovic-Huezo O, Serra V, Majumder PK, Baselga J, Rosen
N.
\newblock {AKT} Inhibition Relieves Feedback Suppression of Receptor Tyrosine
Kinase Expression and Activity.
\newblock Cancer Cell. 2011 Jan; 19(1):58--71.
\bibitem[{Bailey et~al.(2014)Bailey, Sean T and Zhou, Bing and Damrauer,
Jeffrey S and Krishnan, Bhavani and Wilson, Harper L and Smith, Aleisha M and
Li, Mingqing and Yeh, Jen Jen and Kim, William Y}]{Bailey2014-pd}
\textbf{\color{eLifeMediumGrey} Bailey ST}, Zhou B, Damrauer JS, Krishnan B,
Wilson HL, Smith AM, Li M, Yeh JJ, Kim WY.
\newblock {mTOR} Inhibition Induces Compensatory, Therapeutically Targetable
{MEK} Activation in Renal Cell Carcinoma.
\newblock PLoS One. 2014 Sep; 9(9):e104413.
\bibitem[{Littlefield et~al.(2014)Littlefield, Peter and Moasser, Mark~M. and
Jura, Natalia}]{Littlefield:Chem.Biol.:2014}
\textbf{\color{eLifeMediumGrey} Littlefield P}, Moasser MM, Jura N.
\newblock {{RETRACTED}}: {{An ATP}}-{{Competitive Inhibitor Modulates}} the
{{Allosteric Function}} of the {{HER3 Pseudokinase}}.
\newblock Chem Biol. 2014 Apr; 21(4):453--458.
\newblock \href{10.1016/j.chembiol.2014.02.011}{\doiprefix
\detokenize{10.1016/j.chembiol.2014.02.011}}.
\bibitem[{{Yun, Cai-Hong} et~al.(2007){Yun, Cai-Hong} and {Boggon, Titus J} and
{Li, Yiqun} and {Woo, Michele S} and {Greulich, Heidi} and {Meyerson,
Matthew} and {Eck, Michael J}}]{Yun:2007jz}
\textbf{\color{eLifeMediumGrey} {Yun, Cai-Hong}}, {Boggon, Titus J}, {Li,
Yiqun}, {Woo, Michele S}, {Greulich, Heidi}, {Meyerson, Matthew}, {Eck,
Michael J}.
\newblock {Structures of lung cancer-derived EGFR mutants and inhibitor
complexes: mechanism of activation and insights into differential inhibitor
sensitivity.}
\newblock Cancer Cell. 2007 Mar; 11(3):217--227.
\bibitem[{Gajiwala et~al.(2013)Gajiwala, Ketan S and Feng, Junli and Ferre,
RoseAnn and Ryan, Kevin and Brodsky, Oleg and Weinrich, Scott and Kath, John
C and Al Stewart}]{Gajiwala:2013bn}
\textbf{\color{eLifeMediumGrey} Gajiwala KS}, Feng J, Ferre R, Ryan K, Brodsky
O, Weinrich S, Kath JC, Stewart A.
\newblock {Insights into the Aberrant Activity of Mutant EGFR Kinase Domain and
Drug Recognition}.
\newblock Structure. 2013; 21(2):209--219.
\bibitem[{Jia et~al.(2016)Jia, Yong and Yun, Cai-Hong and Park, Eunyoung and
Ercan, Dalia and Manuia, Mari and Juarez, Jose and Xu, Chunxiao and Rhee,
Kevin and Chen, Ting and Zhang, Haikuo and Palakurthi, Sangeetha and Jang,
Jaebong and Lelais, Gerald and DiDonato, Michael and Bursulaya, Badry and
Michellys, Pierre-Yves and Epple, Robert and Marsilje, Thomas H and McNeill,
Matthew and Lu, Wenshuo and Harris, Jennifer and Bender, Steven and Wong,
Kwok-Kin and J{\"a}nne, Pasi A and Eck, Michael J}]{Jia:2016di}
\textbf{\color{eLifeMediumGrey} Jia Y}, Yun CH, Park E, Ercan D, Manuia M,
Juarez J, Xu C, Rhee K, Chen T, Zhang H, Palakurthi S, Jang J, Lelais G,
DiDonato M, Bursulaya B, Michellys PY, Epple R, Marsilje TH, McNeill M, Lu W,
et~al.
\newblock {Overcoming EGFR(T790M) and EGFR(C797S) resistance with
mutant-selective allosteric inhibitors}.
\newblock Nature. 2016 Jun; 534(7605):129--132.
\bibitem[{Politi et~al.(2015)Politi, Katerina and Ayeni, Deborah and Lynch,
Thomas}]{Politi:2015fg}
\textbf{\color{eLifeMediumGrey} Politi K}, Ayeni D, Lynch T.
\newblock {The Next Wave of EGFR Tyrosine Kinase Inhibitors Enter the Clinic.}
\newblock Cancer Cell. 2015 Jun; 27(6):751--753.
\bibitem[{Song et~al.(2015{\natexlab{a}})Song, Zilan and Wang, Meining and
Zhang, Ao}]{Song:2015gu}
\textbf{\color{eLifeMediumGrey} Song Z}, Wang M, Zhang A.
\newblock {Alectinib: a novel second generation anaplastic lymphoma kinase
(ALK) inhibitor for overcoming clinically-acquired resistance}.
\newblock Acta Pharmaceutica Sinica B. 2015 Jan; 5(1):34--37.
\bibitem[{Varghese and Berger(2014)Varghese, Anna M and Berger, Michael
F}]{Varghese:2014jw}
\textbf{\color{eLifeMediumGrey} Varghese AM}, Berger MF.
\newblock {Advancing clinical oncology through genome biology and technology.}
\newblock Genome biology. 2014 Aug; 15(8):427.
\bibitem[{Zehir et~al.(2017{\natexlab{a}})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}]{Zehir:2017ib}
\textbf{\color{eLifeMediumGrey} Zehir A}, Benayed R, Shah RH, Syed A, Middha S,
Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron
DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J,
Mandelker DL, et~al.
\newblock {Mutational landscape of metastatic cancer revealed from prospective
clinical sequencing of 10,000 patients.}
\newblock Nature medicine. 2017 May; 159:676.
\bibitem[{Garraway(2013)Garraway, Levi A}]{Garraway:2013kn}
\textbf{\color{eLifeMediumGrey} Garraway LA}.
\newblock {Genomics-driven oncology: framework for an emerging paradigm.}
\newblock Journal of clinical oncology : official journal of the American
Society of Clinical Oncology. 2013 May; 31(15):1806--1814.
\bibitem[{Hauser et~al.(2018)Hauser, Kevin and Negron, Christopher and
Albanese, Steven K and Ray, Soumya and Steinbrecher, Thomas and Abel, Robert
and Chodera, John D and Wang, Lingle}]{Hauser:2018vz}
\textbf{\color{eLifeMediumGrey} Hauser K}, Negron C, Albanese SK, Ray S,
Steinbrecher T, Abel R, Chodera JD, Wang L.
\newblock {Predicting resistance of clinical Abl mutations to targeted kinase
inhibitors using alchemical free-energy calculations}.
\newblock Communications Biology. 2018 Jun; 1(1):70.
\bibitem[{Durrant and McCammon(2011)Durrant, Jacob D and McCammon, J
Andrew}]{Durrant:2011bm}
\textbf{\color{eLifeMediumGrey} Durrant JD}, McCammon JA.
\newblock {Molecular dynamics simulations and drug discovery.}
\newblock BMC biology. 2011; 9(1):71.
\bibitem[{Lin et~al.(2003)Lin, Jung Hsin and Perryman, Alexander L and Schames,
Julie R and McCammon, J Andrew}]{Lin:2003im}
\textbf{\color{eLifeMediumGrey} Lin JH}, Perryman AL, Schames JR, McCammon JA.
\newblock {The relaxed complex method: Accommodating receptor flexibility for
drug design with an improved scoring scheme}.
\newblock Biopolymers. 2003 Jan; 68(1):47--62.
\bibitem[{Kitchen et~al.(2004)Kitchen, Douglas B and Decornez, H{\'e}l{\`e}ne
and Furr, John R and Bajorath, J{\"u}rgen}]{Kitchen:2004hq}
\textbf{\color{eLifeMediumGrey} Kitchen DB}, Decornez H, Furr JR, Bajorath J.
\newblock {Docking and scoring in virtual screening for drug discovery: methods
and applications}.
\newblock Nature reviews Drug discovery. 2004 Nov; 3(11):935--949.
\bibitem[{Amaro et~al.(2008)Amaro, Rommie E and Baron, Riccardo and McCammon, J
Andrew}]{Amaro:2008hk}
\textbf{\color{eLifeMediumGrey} Amaro RE}, Baron R, McCammon JA.
\newblock {An improved relaxed complex scheme for receptor flexibility in
computer-aided drug design}.
\newblock Journal of computer-aided molecular design. 2008 Jan;
22(9):693--705.
\bibitem[{Hazuda et~al.(2004)Hazuda, Daria J and Anthony, Neville J and Gomez,
Robert P and Jolly, Samson M and Wai, John S and Zhuang, Linghang and Fisher,
Thorsten E and Embrey, Mark and Guare, James P and Egbertson, Melissa S and
Vacca, Joseph P and Huff, Joel R and Felock, Peter J and Witmer, Marc V and
Stillmock, Kara A and Danovich, Robert and Grobler, Jay and Miller, Michael D
and Espeseth, Amy S and Jin, Lixia and Chen, I-Wu and Lin, Jiunn H and
Kassahun, Kelem and Ellis, Joan D and Wong, Bradley K and Xu, Wei and
Pearson, Paul G and Schleif, William A and Cortese, Riccardo and Emini,
Emilio and Summa, Vincenzo and Holloway, M Katharine and Young, Steven
D}]{Hazuda:2004ja}
\textbf{\color{eLifeMediumGrey} Hazuda DJ}, Anthony NJ, Gomez RP, Jolly SM, Wai
JS, Zhuang L, Fisher TE, Embrey M, Guare JP, Egbertson MS, Vacca JP, Huff JR,
Felock PJ, Witmer MV, Stillmock KA, Danovich R, Grobler J, Miller MD,
Espeseth AS, Jin L, et~al.
\newblock {A naphthyridine carboxamide provides evidence for discordant
resistance between mechanistically identical inhibitors of HIV-1 integrase}.
\newblock Proceedings of the National Academy of Sciences. 2004 Aug;
101(31):11233--11238.
\bibitem[{Norman et~al.(2012)Norman, Richard A and Toader, Dorin and Ferguson,
Andrew D}]{Norman:2012gwa}
\textbf{\color{eLifeMediumGrey} Norman RA}, Toader D, Ferguson AD.
\newblock {Structural approaches to obtain kinase selectivity}.
\newblock Trends in pharmacological sciences. 2012 May; 33(5):273--278.
\bibitem[{Shoichet(2004)Shoichet, Brian K}]{Shoichet:2004jha}
\textbf{\color{eLifeMediumGrey} Shoichet BK}.
\newblock {Virtual screening of chemical libraries}.
\newblock Nature. 2004 Dec; 432(7019):862--865.
\bibitem[{Warren et~al.(2006)Warren, Gregory L and Andrews, C Webster and
Capelli, Anna-Maria and Clarke, Brian and LaLonde, Judith and Lambert,
Millard H and Lindvall, Mika and Nevins, Neysa and Semus, Simon F and Senger,
Stefan and Tedesco, Giovanna and Wall, Ian D and Woolven, James M and
Peishoff, Catherine E and Head, Martha S}]{Warren:2006jh}
\textbf{\color{eLifeMediumGrey} Warren GL}, Andrews CW, Capelli AM, Clarke B,
LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G,
Wall ID, Woolven JM, Peishoff CE, Head MS.
\newblock {A Critical Assessment of Docking Programs and Scoring Functions}.
\newblock Journal of medicinal chemistry. 2006 Oct; 49(20):5912--5931.
\bibitem[{Chodera et~al.(2011{\natexlab{a}})Chodera, John D and Mobley, David L
and Shirts, Michael R and Dixon, Richard W and Branson, Kim and Pande, Vijay
S}]{Chodera2011-jn}
\textbf{\color{eLifeMediumGrey} Chodera JD}, Mobley DL, Shirts MR, Dixon RW,
Branson K, Pande VS.
\newblock Alchemical free energy methods for drug discovery: progress and
challenges.
\newblock Curr Opin Struct Biol. 2011 Apr; 21(2):150--160.
\bibitem[{Aldeghi et~al.(2016{\natexlab{a}})Aldeghi, Matteo and Heifetz,
Alexander and Bodkin, Michael J and Knapp, Stefan and Biggin, Philip
C}]{Aldeghi:2016et}
\textbf{\color{eLifeMediumGrey} Aldeghi M}, Heifetz A, Bodkin MJ, Knapp S,
Biggin PC.
\newblock {Accurate calculation of the absolute free energy of binding for drug
molecules.}
\newblock Chemical science. 2016 Jan; 7(1):207--218.
\bibitem[{Mikulskis et~al.(2014)Mikulskis, Paulius and Genheden, Samuel and
Ryde, Ulf}]{Mikulskis:2014df}
\textbf{\color{eLifeMediumGrey} Mikulskis P}, Genheden S, Ryde U.
\newblock {A large-scale test of free-energy simulation estimates of
protein-ligand binding affinities.}
\newblock Journal of chemical information and modeling. 2014 Oct;
54(10):2794--2806.
\bibitem[{Huang and MacKerell(2013)Huang, Jing and MacKerell, Alexander
D.}]{Huang:J.Comput.Chem.:2013}
\textbf{\color{eLifeMediumGrey} Huang J}, MacKerell AD.
\newblock {{CHARMM36}} All-Atom Additive Protein Force Field: {{Validation}}
Based on Comparison to {{NMR}} Data.
\newblock J Comput Chem. 2013 Sep; 34(25):2135--2145.
\newblock \href{10.1002/jcc.23354}{\doiprefix \detokenize{10.1002/jcc.23354}}.
\bibitem[{Maier et~al.(2015)Maier, James A. and Martinez, Carmenza and
Kasavajhala, Koushik and Wickstrom, Lauren and Hauser, Kevin E. and
Simmerling, Carlos}]{Maier:J.Chem.TheoryComput.:2015}
\textbf{\color{eLifeMediumGrey} Maier JA}, Martinez C, Kasavajhala K, Wickstrom
L, Hauser KE, Simmerling C.
\newblock {{ff14SB}}: {{Improving}} the {{Accuracy}} of {{Protein Side Chain}}
and {{Backbone Parameters}} from {{ff99SB}}.
\newblock J Chem Theory Comput. 2015 Aug; 11(8):3696--3713.
\newblock \href{10.1021/acs.jctc.5b00255}{\doiprefix
\detokenize{10.1021/acs.jctc.5b00255}}.
\bibitem[{Harder et~al.(2016)Harder, Edward and Damm, Wolfgang and Maple, Jon
and Wu, Chuanjie and Reboul, Mark and Xiang, Jin Yu and Wang, Lingle and
Lupyan, Dmitry and Dahlgren, Markus K. and Knight, Jennifer L. and Kaus,
Joseph W. and Cerutti, David S. and Krilov, Goran and Jorgensen, William L.
and Abel, Robert and Friesner, Richard A.}]{Harder:J.Chem.TheoryComput.:2016}
\textbf{\color{eLifeMediumGrey} Harder E}, Damm W, Maple J, Wu C, Reboul M,
Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS,
Krilov G, Jorgensen WL, Abel R, Friesner RA.
\newblock {{OPLS3}}: {{A Force Field Providing Broad Coverage}} of
{{Drug}}-like {{Small Molecules}} and {{Proteins}}.
\newblock J Chem Theory Comput. 2016 Jan; 12(1):281--296.
\newblock \href{10.1021/acs.jctc.5b00864}{\doiprefix
\detokenize{10.1021/acs.jctc.5b00864}}.
\bibitem[{Cournia et~al.(2017)Cournia, Zoe and Allen, Bryce and Sherman,
Woody}]{Cournia:2017ip}
\textbf{\color{eLifeMediumGrey} Cournia Z}, Allen B, Sherman W.
\newblock {Relative Binding Free Energy Calculations in Drug Discovery: Recent
Advances and Practical Considerations.}
\newblock Journal of chemical information and modeling. 2017 Dec;
57(12):2911--2937.
\bibitem[{Brown et~al.(2009)Brown, Scott P. and Muchmore, Steven W. and Hajduk,
Philip J.}]{BROWN2009420}
\textbf{\color{eLifeMediumGrey} Brown SP}, Muchmore SW, Hajduk PJ.
\newblock Healthy Skepticism: Assessing Realistic Model Performance.
\newblock Drug Discov Today. 2009; 14(7):420 -- 427.
\newblock \href{http://dx.doi.org/10.1016/j.drudis.2009.01.012}{\doiprefix
\detokenize{http://dx.doi.org/10.1016/j.drudis.2009.01.012}}.
\bibitem[{Abel et~al.(2017{\natexlab{a}})Abel, Robert and Mondal, Sayan and
Masse, Craig and Greenwood, Jeremy and Harriman, Geraldine and Ashwell, Mark
A and Bhat, Sathesh and Wester, Ronald and Frye, Leah and Kapeller, Rosana
and Friesner, Richard A}]{Abel2017-gw}
\textbf{\color{eLifeMediumGrey} Abel R}, Mondal S, Masse C, Greenwood J,
Harriman G, Ashwell MA, Bhat S, Wester R, Frye L, Kapeller R, Friesner RA.
\newblock Accelerating drug discovery through tight integration of expert
molecular design and predictive scoring.
\newblock Curr Opin Struct Biol. 2017 Apr; 43(Supplement C):38--44.
\bibitem[{Lovering et~al.(2016{\natexlab{a}})Lovering, Frank and Aevazelis,
Cristina and Chang, Jeanne and Dehnhardt, Christoph and Fitz, Lori and Han,
Seungil and Janz, Kristin and Lee, Julie and Kaila, Neelu and McDonald,
Joseph and Moore, William and Moretto, Alessandro and Papaioannou, Nikolaos
and Richard, David and Ryan, Mark S and Wan, Zhao-Kui and Thorarensen,
Atli}]{Lovering:2016fg}
\textbf{\color{eLifeMediumGrey} Lovering F}, Aevazelis C, Chang J, Dehnhardt C,
Fitz L, Han S, Janz K, Lee J, Kaila N, McDonald J, Moore W, Moretto A,
Papaioannou N, Richard D, Ryan MS, Wan ZK, Thorarensen A.
\newblock {Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified
by Free-Energy Perturbation (FEP).}
\newblock ChemMedChem. 2016 Jan; 11(2):217--233.
\bibitem[{Ciordia et~al.(2016)Ciordia, Myriam and P{\'e}rez-Benito, Laura and
Delgado, Francisca and Trabanco, Andr{\'e}s A and Tresadern,
Gary}]{Ciordia:2016dn}
\textbf{\color{eLifeMediumGrey} Ciordia M}, P{\'e}rez-Benito L, Delgado F,
Trabanco AA, Tresadern G.
\newblock {Application of Free Energy Perturbation for the Design of BACE1
Inhibitors.}
\newblock Journal of chemical information and modeling. 2016 Sep;
56(9):1856--1871.
\bibitem[{Lenselink et~al.(2016)Lenselink, Eelke B and Louvel, Julien and
Forti, Anna F and van Veldhoven, Jacobus P D and de Vries, Henk and
Mulder-Krieger, Thea and McRobb, Fiona M and Negri, Ana and Goose, Joseph and
Abel, Robert and van Vlijmen, Herman W T and Wang, Lingle and Harder, Edward
and Sherman, Woody and IJzerman, Adriaan P and Beuming,
Thijs}]{Lenselink:2016ip}
\textbf{\color{eLifeMediumGrey} Lenselink EB}, Louvel J, Forti AF, van
Veldhoven JPD, de~Vries H, Mulder-Krieger T, McRobb FM, Negri A, Goose J,
Abel R, van Vlijmen HWT, Wang L, Harder E, Sherman W, IJzerman AP, Beuming T.
\newblock {Predicting Binding Affinities for GPCR Ligands Using Free-Energy
Perturbation.}
\newblock ACS omega. 2016 Aug; 1(2):293--304.
\bibitem[{Jorgensen(2016)Jorgensen, William L}]{Jorgensen:2016dv}
\textbf{\color{eLifeMediumGrey} Jorgensen WL}.
\newblock {Computer-aided discovery of anti-HIV agents.}
\newblock Bioorganic {\&} medicinal chemistry. 2016 Oct; 24(20):4768--4778.
\bibitem[{Lin et~al.(2013)Lin, Yen-Lin and Meng, Yilin and Jiang, Wei and Roux,
Beno{\^\i}t}]{Lin2013-ft}
\textbf{\color{eLifeMediumGrey} Lin YL}, Meng Y, Jiang W, Roux B.
\newblock Explaining why Gleevec is a specific and potent inhibitor of Abl
kinase.
\newblock Proc Natl Acad Sci U S A. 2013 Jan; 110(5):1664--1669.
\bibitem[{Lin et~al.(2014)Lin, Yen-Lin and Meng, Yilin and Huang, Lei and Roux,
Beno{\^\i}t}]{Lin2014-iv}
\textbf{\color{eLifeMediumGrey} Lin YL}, Meng Y, Huang L, Roux B.
\newblock Computational Study of Gleevec and {G6G} Reveals Molecular
Determinants of Kinase Inhibitor Selectivity.
\newblock J Am Chem Soc. 2014 Oct; 136(42):14753--14762.
\bibitem[{Aldeghi et~al.(2017)Aldeghi, Matteo and Heifetz, Alexander and
Bodkin, Michael J and Knapp, Stefan and Biggin, Philip C}]{Aldeghi2017-ox}
\textbf{\color{eLifeMediumGrey} Aldeghi M}, Heifetz A, Bodkin MJ, Knapp S,
Biggin PC.
\newblock Predictions of Ligand Selectivity from Absolute Binding Free Energy
Calculations.
\newblock J Am Chem Soc. 2017 Jan; 139(2):946--957.
\bibitem[{Shan et~al.(2012)Shan, Yibing and Eastwood, Michael P and Zhang,
Xuewu and Kim, Eric T and Arkhipov, Anton and Dror, Ron O and Jumper, John
and Kuriyan, John and Shaw, David E}]{Shan:2012bs}
\textbf{\color{eLifeMediumGrey} Shan Y}, Eastwood MP, Zhang X, Kim ET, Arkhipov
A, Dror RO, Jumper J, Kuriyan J, Shaw DE.
\newblock {Oncogenic mutations counteract intrinsic disorder in the EGFR kinase
and promote receptor dimerization.}
\newblock Cell. 2012 May; 149(4):860--870.
\bibitem[{Sutto and Gervasio(2013)Sutto, Ludovico and Gervasio, Francesco
Luigi}]{Sutto:2013gy}
\textbf{\color{eLifeMediumGrey} Sutto L}, Gervasio FL.
\newblock {Effects of oncogenic mutations on the conformational free-energy
landscape of EGFR kinase.}
\newblock Proceedings of the National Academy of Sciences of the United States
of America. 2013 Jun; 110(26):10616--10621.
\bibitem[{Park et~al.(2016)Park, Jiyong and McDonald, Joseph J and Petter,
Russell C and Houk, K N}]{Park:2016ip}
\textbf{\color{eLifeMediumGrey} Park J}, McDonald JJ, Petter RC, Houk KN.
\newblock {Molecular Dynamics Analysis of Binding of Kinase Inhibitors to WT
EGFR and the T790M Mutant}.
\newblock Journal of Chemical Theory and Computation. 2016 Apr;
12(4):2066--2078.
\bibitem[{Demir et~al.(2011)Demir, {\"O}zlem and Baronio, Roberta and Salehi,
Faezeh and Wassman, Christopher D and Hall, Linda and Hatfield, G Wesley and
Chamberlin, Richard and Kaiser, Peter and Lathrop, Richard H and Amaro,
Rommie E}]{Demir:2011bc}
\textbf{\color{eLifeMediumGrey} Demir {\"O}}, Baronio R, Salehi F, Wassman CD,
Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro RE.
\newblock {Ensemble-based computational approach discriminates functional
activity of p53 cancer and rescue mutants.}
\newblock PLoS Computational Biology. 2011 Oct; 7(10):e1002238.
\bibitem[{Witham et~al.(2011)Witham, Shawn and Takano, Kyoko and Schwartz,
Charles and Alexov, Emil}]{Witham:2011co}
\textbf{\color{eLifeMediumGrey} Witham S}, Takano K, Schwartz C, Alexov E.
\newblock {A missense mutation in CLIC2 associated with intellectual disability
is predicted by in silico modeling to affect protein stability and dynamics.}
\newblock Proteins. 2011 Aug; 79(8):2444--2454.
\bibitem[{Tsukamoto and Farrens(2013)Tsukamoto, Hisao and Farrens, David
L}]{Tsukamoto:2013gr}
\textbf{\color{eLifeMediumGrey} Tsukamoto H}, Farrens DL.
\newblock {A constitutively activating mutation alters the dynamics and
energetics of a key conformational change in a ligand-free G protein-coupled
receptor.}
\newblock The Journal of biological chemistry. 2013 Sep; 288(39):28207--28216.
\bibitem[{Seeliger and de~Groot(2010)Seeliger, Daniel and de Groot, Bert
L}]{Seeliger:2010hn}
\textbf{\color{eLifeMediumGrey} Seeliger D}, de~Groot BL.
\newblock {Protein thermostability calculations using alchemical free energy
simulations.}
\newblock Biophysical journal. 2010 May; 98(10):2309--2316.
\bibitem[{Steinbrecher et~al.(2017{\natexlab{a}})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}]{Steinbrecher:2017ge}
\textbf{\color{eLifeMediumGrey} Steinbrecher T}, Zhu C, Wang L, Abel R, Negron
C, Pearlman D, Feyfant E, Duan J, Sherman W.
\newblock {Predicting the Effect of Amino Acid Single-Point Mutations on
Protein Stability{\textemdash}Large-Scale Validation of MD-Based Relative
Free Energy Calculations}.
\newblock Journal of Molecular Biology. 2017 Apr; 429(7):948--963.
\bibitem[{Ford and Babaoglu(2017{\natexlab{a}})Ford, Melissa Coates and
Babaoglu, Kerim}]{Ford:2017bn}
\textbf{\color{eLifeMediumGrey} Ford MC}, Babaoglu K.
\newblock {Examining the Feasibility of Using Free Energy Perturbation (FEP+)
in Predicting Protein Stability}.
\newblock Journal of chemical information and modeling. 2017 Jun;
57(6):1276--1285.
\bibitem[{Mondal et~al.(2016{\natexlab{a}})Mondal, Jagannath and Tiwary,
Pratyush and Berne, B J}]{Mondal:2016ju}
\textbf{\color{eLifeMediumGrey} Mondal J}, Tiwary P, Berne BJ.
\newblock {How a Kinase Inhibitor Withstands Gatekeeper Residue Mutations.}
\newblock Journal of the American Chemical Society. 2016 Apr;
138(13):4608--4615.
\bibitem[{Fan et~al.(2007)Fan, Qi-Wen and Cheng, Christine K and Nicolaides,
Theodore P and Hackett, Christopher S and Knight, Zachary A and Shokat, Kevan
M and Weiss, William A}]{Fan2007-hm}
\textbf{\color{eLifeMediumGrey} Fan QW}, Cheng CK, Nicolaides TP, Hackett CS,
Knight ZA, Shokat KM, Weiss WA.
\newblock A dual phosphoinositide-3-kinase {alpha/mTOR} inhibitor cooperates
with blockade of epidermal growth factor receptor in {PTEN-mutant} glioma.
\newblock Cancer Res. 2007 Sep; 67(17):7960--7965.
\bibitem[{Kijima et~al.(2011)Kijima, Takashi and Shimizu, Tomohito and Nonen,
Shinpei and Furukawa, Mitsugi and Otani, Yasushi and Minami, Toshiyuki and
Takahashi, Ryo and Hirata, Haruhiko and Nagatomo, Izumi and Takeda, Yoshito
and Kida, Hiroshi and Goya, Sho and Fujio, Yasushi and Azuma, Junichi and
Tachibana, Isao and Kawase, Ichiro}]{Kijima2011-xs}
\textbf{\color{eLifeMediumGrey} Kijima T}, Shimizu T, Nonen S, Furukawa M,
Otani Y, Minami T, Takahashi R, Hirata H, Nagatomo I, Takeda Y, Kida H, Goya
S, Fujio Y, Azuma J, Tachibana I, Kawase I.
\newblock Safe and successful treatment with erlotinib after gefitinib-induced
hepatotoxicity: difference in metabolism as a possible mechanism.
\newblock J Clin Oncol. 2011 Jul; 29(19):e588--90.
\bibitem[{Lin and Roux(2013)Lin, Yen-Lin and Roux, Beno{\^\i}t}]{Lin2013-mu}
\textbf{\color{eLifeMediumGrey} Lin YL}, Roux B.
\newblock Computational Analysis of the Binding Specificity of Gleevec to Abl,
c-Kit, Lck, and c-Src Tyrosine Kinases.
\newblock J Am Chem Soc. 2013 Oct; 135(39):14741--14753.
\bibitem[{Wang et~al.(2015)Wang, Lingle and Wu, Yujie and Deng, Yuqing and Kim,
Byungchan and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson,
Shaughnessy and Dahlgren, Markus K. and Greenwood, Jeremy and Romero, Donna
L. and Masse, Craig and Knight, Jennifer L. and Steinbrecher, Thomas and
Beuming, Thijs and Damm, Wolfgang and Harder, Ed and Sherman, Woody and
Brewer, Mark and Wester, Ron and Murcko, Mark and Frye, Leah and Farid, Ramy
and Lin, Teng and Mobley, David L. and Jorgensen, William L. and Berne, Bruce
J. and Friesner, Richard A. and Abel, Robert}]{Wang:J.Am.Chem.Soc.:2015}
\textbf{\color{eLifeMediumGrey} Wang L}, Wu Y, Deng Y, Kim B, Pierce L, Krilov
G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight
JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester
R, et~al.
\newblock Accurate and {{Reliable Prediction}} of {{Relative Ligand Binding
Potency}} in {{Prospective Drug Discovery}} by {{Way}} of a {{Modern
Free}}-{{Energy Calculation Protocol}} and {{Force Field}}.
\newblock J Am Chem Soc. 2015 Feb; 137(7):2695--2703.
\newblock \href{10.1021/ja512751q}{\doiprefix \detokenize{10.1021/ja512751q}}.
\bibitem[{Abel et~al.(2017{\natexlab{b}})Abel, Robert and Wang, Lingle and
Harder, Edward D and Berne, B J and Friesner, Richard A}]{Abel:2017jt}
\textbf{\color{eLifeMediumGrey} Abel R}, Wang L, Harder ED, Berne BJ, Friesner
RA.
\newblock {Advancing Drug Discovery through Enhanced Free Energy Calculations.}
\newblock Accounts of chemical research. 2017 Jul; 50(7):1625--1632.
\bibitem[{Pao et~al.(2004)Pao, William and Miller, Vincent and Zakowski,
Maureen and Doherty, Jennifer and Politi, Katerina and Sarkaria, Inderpal and
Singh, Bhuvanesh and Heelan, Robert and Rusch, Valerie and Fulton, Lucinda
and Mardis, Elaine and Kupfer, Doris and Wilson, Richard and Kris, Mark and
Varmus, Harold}]{Pao2004-kx}
\textbf{\color{eLifeMediumGrey} Pao W}, Miller V, Zakowski M, Doherty J, Politi
K, Sarkaria I, Singh B, Heelan R, Rusch V, Fulton L, Mardis E, Kupfer D,
Wilson R, Kris M, Varmus H.
\newblock {EGF} receptor gene mutations are common in lung cancers from ``never
smokers'' and are associated with sensitivity of tumors to gefitinib and
erlotinib.
\newblock Proceedings of the National Academy of Sciences. 2004 Sep;
101(36):13306--13311.
\bibitem[{Kim et~al.(2012)Kim, Youngjoo and Li, Zhimin and Apetri, Mihaela and
Luo, Beibei and Settleman, Jeffrey E and Anderson, Karen S}]{Kim2012-mo}
\textbf{\color{eLifeMediumGrey} Kim Y}, Li Z, Apetri M, Luo B, Settleman JE,
Anderson KS.
\newblock Temporal resolution of autophosphorylation for normal and oncogenic
forms of {EGFR} and differential effects of gefitinib.
\newblock Biochemistry. 2012 Jun; 51(25):5212--5222.
\bibitem[{Juchum et~al.(2015)Juchum, Michael and G{\"u}nther, Marcel and
Laufer, Stefan A.}]{Juchum:DrugResist.Updat.:2015}
\textbf{\color{eLifeMediumGrey} Juchum M}, G{\"u}nther M, Laufer SA.
\newblock Fighting Cancer Drug Resistance: {{Opportunities}} and Challenges for
Mutation-Specific {{EGFR}} Inhibitors.
\newblock Drug Resist Updat. 2015 May; 20:12--28.
\newblock \href{10.1016/j.drup.2015.05.002}{\doiprefix
\detokenize{10.1016/j.drup.2015.05.002}}.
\bibitem[{Din and Woll(2008)Din, Omar S and Woll, Penella J}]{Din2008-ag}
\textbf{\color{eLifeMediumGrey} Din OS}, Woll PJ.
\newblock Treatment of gastrointestinal stromal tumor: focus on imatinib
mesylate.
\newblock Ther Clin Risk Manag. 2008 Feb; 4(1):149--162.
\bibitem[{Santos et~al.(2016)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.}]{Santos:Nat.Rev.DrugDiscov.:2016}
\textbf{\color{eLifeMediumGrey} Santos R}, Ursu O, Gaulton A, Bento AP, Donadi
RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI, Overington JP.
\newblock A Comprehensive Map of Molecular Drug Targets.
\newblock Nat Rev Drug Discov. 2016 Dec; 16(1):19--34.
\newblock \href{10.1038/nrd.2016.230}{\doiprefix
\detokenize{10.1038/nrd.2016.230}}.
\bibitem[{Volkamer et~al.(2015{\natexlab{a}})Volkamer, Andrea and Eid, Sameh
and Turk, Samo and Jaeger, Sabrina and Rippmann, Friedrich and Fulle,
Simone}]{Volkamer2015-jx}
\textbf{\color{eLifeMediumGrey} Volkamer A}, Eid S, Turk S, Jaeger S, Rippmann
F, Fulle S.
\newblock Pocketome of human kinases: prioritizing the {ATP} binding sites of
(yet) untapped protein kinases for drug discovery.
\newblock J Chem Inf Model. 2015 Mar; 55(3):538--549.
\bibitem[{Wu et~al.(2015{\natexlab{a}})Wu, Peng and Nielsen, Thomas E and
Clausen, Mads H}]{Wu2015-oq}
\textbf{\color{eLifeMediumGrey} Wu P}, Nielsen TE, Clausen MH.
\newblock {FDA-approved} small-molecule kinase inhibitors.
\newblock Trends Pharmacol Sci. 2015 Jul; 36(7):422--439.
\bibitem[{Volkamer et~al.(2016)Volkamer, Andrea and Eid, Sameh and Turk, Samo
and Rippmann, Friedrich and Fulle, Simone}]{Volkamer2016-sj}
\textbf{\color{eLifeMediumGrey} Volkamer A}, Eid S, Turk S, Rippmann F, Fulle
S.
\newblock Identification and Visualization of {Kinase-Specific} Subpockets.
\newblock J Chem Inf Model. 2016 Feb; 56(2):335--346.
\bibitem[{Christmann-Franck et~al.(2016)Christmann-Franck, Serge and van
Westen, Gerard J P and Papadatos, George and Beltran Escudie, Fanny and
Roberts, Alexander and Overington, John P and Domine,
Daniel}]{ChristmannFranck:2016gka}
\textbf{\color{eLifeMediumGrey} Christmann-Franck S}, van Westen GJP, Papadatos
G, Beltran~Escudie F, Roberts A, Overington JP, Domine D.
\newblock {Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate
Prediction of Compound{\textendash}Kinase Activities: A Way toward Selective
Promiscuity by Design?}
\newblock Journal of chemical information and modeling. 2016 Sep;
56(9):1654--1675.
\bibitem[{Anastassiadis et~al.(2011)Anastassiadis, Theonie and Deacon, Sean W
and Devarajan, Karthik and Ma, Haiching and Peterson, Jeffrey
R}]{Anastassiadis2011-sm}
\textbf{\color{eLifeMediumGrey} Anastassiadis T}, Deacon SW, Devarajan K, Ma H,
Peterson JR.
\newblock Comprehensive assay of kinase catalytic activity reveals features of
kinase inhibitor selectivity.
\newblock Nat Biotechnol. 2011 Nov; 29(11):1039--1045.
\bibitem[{Klaeger et~al.(2017)Klaeger, Susan and Heinzlmeir, Stephanie and
Wilhelm, Mathias and Polzer, Harald and Vick, Binje and Koenig, Paul-Albert
and Reinecke, Maria and Ruprecht, Benjamin and Petzoldt, Svenja and Meng,
Chen and Zecha, Jana and Reiter, Katrin and Qiao, Huichao and Helm, Dominic
and Koch, Heiner and Schoof, Melanie and Canevari, Giulia and Casale, Elena
and Depaolini, Stefania Re and Feuchtinger, Annette and Wu, Zhixiang and
Schmidt, Tobias and Rueckert, Lars and Becker, Wilhelm and Huenges, Jan and
Garz, Anne-Kathrin and Gohlke, Bjoern-Oliver and Zolg, Daniel Paul and
Kayser, Gian and Vooder, Tonu and Preissner, Robert and Hahne, Hannes and
T{\~o}nisson, Neeme and Kramer, Karl and G{\"o}tze, Katharina and Bassermann,
Florian and Schlegl, Judith and Ehrlich, Hans-Christian and Aiche, Stephan
and Walch, Axel and Greif, Philipp A and Schneider, Sabine and Felder, Eduard
Rudolf and Ruland, Juergen and M{\'e}dard, Guillaume and Jeremias, Irmela and
Spiekermann, Karsten and Kuster, Bernhard}]{Klaeger2017-jr}
\textbf{\color{eLifeMediumGrey} Klaeger S}, Heinzlmeir S, Wilhelm M, Polzer H,
Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J,
Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini
SR, Feuchtinger A, et~al.
\newblock The target landscape of clinical kinase drugs.
\newblock Science. 2017 Dec; 358(6367).
\bibitem[{Sun et~al.(2014)Sun, Chong and Hobor, Sebastijan and Bertotti, Andrea
and Zecchin, Davide and Huang, Sidong and Galimi, Francesco and Cottino,
Francesca and Prahallad, Anirudh and Grernrum, Wipawadee and Tzani, Anna and
Schlicker, Andreas and Wessels, Lodewyk F A and Smit, Egbert F and
Thunnissen, Erik and Halonen, Pasi and Lieftink, Cor and Beijersbergen,
Roderick L and Di Nicolantonio, Federica and Bardelli, Alberto and Trusolino,
Livio and Bernards, Ren{\'e}}]{Sun:2014kt}
\textbf{\color{eLifeMediumGrey} Sun C}, Hobor S, Bertotti A, Zecchin D, Huang
S, Galimi F, Cottino F, Prahallad A, Grernrum W, Tzani A, Schlicker A,
Wessels LFA, Smit EF, Thunnissen E, Halonen P, Lieftink C, Beijersbergen RL,
Di~Nicolantonio F, Bardelli A, Trusolino L, et~al.
\newblock {Intrinsic resistance to MEK inhibition in KRAS mutant lung and colon
cancer through transcriptional induction of ERBB3.}
\newblock CellReports. 2014 Apr; 7(1):86--93.
\bibitem[{Manchado et~al.(2016)Manchado, Eusebio and Weissmueller, Susann and
Morris, John P and Chen, Chi-Chao and Wullenkord, Ramona and Lujambio, Amaia
and de Stanchina, Elisa and Poirier, John T and Gainor, Justin F and
Corcoran, Ryan B and Engelman, Jeffrey A and Rudin, Charles M and Rosen, Neal
and Lowe, Scott W}]{Manchado:2016fb}
\textbf{\color{eLifeMediumGrey} Manchado E}, Weissmueller S, Morris JP, Chen
CC, Wullenkord R, Lujambio A, de~Stanchina E, Poirier JT, Gainor JF, Corcoran
RB, Engelman JA, Rudin CM, Rosen N, Lowe SW.
\newblock {A combinatorial strategy for treating KRAS-mutant lung cancer.}
\newblock Nature. 2016 Jun; 534(7609):647--651.
\bibitem[{Shao et~al.(2013)Shao, Hao and Shi, Shenhua and Huang, Shiliang and
Hole, Alison J and Abbas, Abdullahi Y and Baumli, Sonja and Liu, Xiangrui and
Lam, Frankie and Foley, David W and Fischer, Peter M and Noble, Martin and
Endicott, Jane A and Pepper, Chris and Wang, Shudong}]{Shao2013-oe}
\textbf{\color{eLifeMediumGrey} Shao H}, Shi S, Huang S, Hole AJ, Abbas AY,
Baumli S, Liu X, Lam F, Foley DW, Fischer PM, Noble M, Endicott JA, Pepper C,
Wang S.
\newblock Substituted 4-(Thiazol-5-yl)-2-(phenylamino)pyrimidines Are Highly
Active {CDK9} Inhibitors: Synthesis, X-ray Crystal Structures,
{Structure--Activity} Relationship, and Anticancer Activities.
\newblock J Med Chem. 2013 Feb; 56(3):640--659.
\bibitem[{Blake et~al.(2016)Blake, James F and Burkard, Michael and Chan,
Jocelyn and Chen, Huifen and Chou, Kang-Jye and Diaz, Dolores and Dudley,
Danette A and Gaudino, John J and Gould, Stephen E and Grina, Jonas and
Hunsaker, Thomas and Liu, Lichuan and Martinson, Matthew and Moreno, David
and Mueller, Lars and Orr, Christine and Pacheco, Patricia and Qin, Ann and
Rasor, Kevin and Ren, Li and Robarge, Kirk and Shahidi-Latham, Sheerin and
Stults, Jeffrey and Sullivan, Francis and Wang, Weiru and Yin, Jianping and
Zhou, Aihe and Belvin, Marcia and Merchant, Mark and Moffat, John and
Schwarz, Jacob B}]{Blake2016-su}
\textbf{\color{eLifeMediumGrey} Blake JF}, Burkard M, Chan J, Chen H, Chou KJ,
Diaz D, Dudley DA, Gaudino JJ, Gould SE, Grina J, Hunsaker T, Liu L,
Martinson M, Moreno D, Mueller L, Orr C, Pacheco P, Qin A, Rasor K, Ren L,
et~al.
\newblock Discovery of
({S)-1-(1-(4-Chloro-3-fluorophenyl)-2-hydroxyethyl)-4-(2-((1-methyl-1H-pyrazol-5-yl)amino)pyrimidin-4-yl)pyridin-2(1H)-one}
({GDC-0994)}, an Extracellular {Signal-Regulated} Kinase 1/2 ({ERK1/2})
Inhibitor in Early Clinical Development.
\newblock J Med Chem. 2016 Jun; 59(12):5650--5660.
\bibitem[{Bosc et~al.(2017)Bosc, Nicolas and Meyer, Christophe and Bonnet,
Pascal}]{Bosc:2017gs}
\textbf{\color{eLifeMediumGrey} Bosc N}, Meyer C, Bonnet P.
\newblock {The use of novel selectivity metrics in kinase research.}
\newblock BMC bioinformatics. 2017 Jan; 18(1):17.
\bibitem[{Cheng et~al.(2010)Cheng, Alan C and Eksterowicz, John and
Geuns-Meyer, Stephanie and Sun, Yaxiong}]{Cheng2010-ip}
\textbf{\color{eLifeMediumGrey} Cheng AC}, Eksterowicz J, Geuns-Meyer S, Sun Y.
\newblock Analysis of kinase inhibitor selectivity using a thermodynamics-based
partition index.
\newblock J Med Chem. 2010 Jun; 53(11):4502--4510.
\bibitem[{Shirts et~al.(2009)Michael R. Shirts and David L. Mobley and Scott P.
Brown}]{shirts-mobley-brown:2009:sbdd}
\textbf{\color{eLifeMediumGrey} Shirts MR}, Mobley DL, Brown SP.
\newblock Free energy calculations in structure-based drug design.
\newblock In: \emph{Structure Based Drug Design} Cambridge University Press;
2009.
\bibitem[{Abel et~al.(2018)Abel, Robert and Manas, Eric S and Friesner, Richard
A and Farid, Ramy S and Wang, Lingle}]{Abel:2018ds}
\textbf{\color{eLifeMediumGrey} Abel R}, Manas ES, Friesner RA, Farid RS, Wang
L.
\newblock {Modeling the value of predictive affinity scoring in preclinical
drug discovery.}
\newblock Current opinion in structural biology. 2018 Oct; 52:103--110.
\bibitem[{Abel et~al.(2017{\natexlab{c}})Abel, Robert and Wang, Lingle and
Mobley, David L and Friesner, Richard A}]{Abel:2017jw}
\textbf{\color{eLifeMediumGrey} Abel R}, Wang L, Mobley DL, Friesner RA.
\newblock {A Critical Review of Validation, Blind Testing, and Real- World Use
of Alchemical Protein-Ligand Binding Free Energy Calculations.}
\newblock Current topics in medicinal chemistry. 2017; 17(23):2577--2585.
\bibitem[{Kooistra et~al.(2016)Kooistra, Albert J and Kanev, Georgi K and van
Linden, Oscar P J and Leurs, Rob and de Esch, Iwan J P and de Graaf,
Chris}]{Kooistra:2016fr}
\textbf{\color{eLifeMediumGrey} Kooistra AJ}, Kanev GK, van Linden OPJ, Leurs
R, de~Esch IJP, de~Graaf C.
\newblock {KLIFS: a structural kinase-ligand interaction database}.
\newblock Nucleic acids research. 2016 Jan; 44(D1):D365--D371.
\bibitem[{van Linden et~al.(2014)van Linden, Oscar P J and Kooistra, Albert J
and Leurs, Rob and de Esch, Iwan J P and de Graaf, Chris}]{vanLinden:2014ea}
\textbf{\color{eLifeMediumGrey} van Linden OPJ}, Kooistra AJ, Leurs R, de~Esch
IJP, de~Graaf C.
\newblock {KLIFS: a knowledge-based structural database to navigate
kinase-ligand interaction space.}
\newblock Journal of medicinal chemistry. 2014 Jan; 57(2):249--277.
\bibitem[{Hole et~al.(2013)Hole, Alison J and Baumli, Sonja and Shao, Hao and
Shi, Shenhua and Huang, Shiliang and Pepper, Chris and Fischer, Peter M and
Wang, Shudong and Endicott, Jane A and Noble, Martin E}]{Hole2013-sr}
\textbf{\color{eLifeMediumGrey} Hole AJ}, Baumli S, Shao H, Shi S, Huang S,
Pepper C, Fischer PM, Wang S, Endicott JA, Noble ME.
\newblock Comparative Structural and Functional Studies of
4-(Thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile {CDK9} Inhibitors
Suggest the Basis for Isotype Selectivity.
\newblock J Med Chem. 2013 Feb; 56(3):660--670.
\bibitem[{Kalliokoski et~al.(2013)Kalliokoski, Tuomo and Kramer, Christian and
Vulpetti, Anna and Gedeck, Peter}]{Kalliokoski:PloSOne:2013}
\textbf{\color{eLifeMediumGrey} Kalliokoski T}, Kramer C, Vulpetti A, Gedeck P.
\newblock Comparability of Mixed {{IC50}} Data\textendash{}a Statistical
Analysis.
\newblock PloS One. 2013; 8(4):e61007.
\bibitem[{Hari et~al.(2013)Hari, Sanjay B and Merritt, Ethan A and Maly, Dustin
J}]{Hari:2013dp}
\textbf{\color{eLifeMediumGrey} Hari SB}, Merritt EA, Maly DJ.
\newblock {Sequence determinants of a specific inactive protein kinase
conformation.}
\newblock Chemistry {\&} biology. 2013 Jun; 20(6):806--815.
\bibitem[{Davis et~al.(2011{\natexlab{b}})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}]{Davis2011-dz}
\textbf{\color{eLifeMediumGrey} Davis MI}, Hunt JP, Herrgard S, Ciceri P,
Wodicka LM, Pallares G, Hocker M, Treiber DK, Zarrinkar PP.
\newblock Comprehensive analysis of kinase inhibitor selectivity.
\newblock Nat Biotechnol. 2011 Oct; 29(11):1046--1051.
\bibitem[{Graczyk(2007)Graczyk, Piotr P}]{Graczyk:2007bm}
\textbf{\color{eLifeMediumGrey} Graczyk PP}.
\newblock {Gini coefficient: a new way to express selectivity of kinase
inhibitors against a family of kinases.}
\newblock Journal of medicinal chemistry. 2007 Nov; 50(23):5773--5779.
\bibitem[{Duong-Ly et~al.(2016)Duong-Ly, Krisna C and Devarajan, Karthik and
Liang, Shuguang and Horiuchi, Kurumi Y and Wang, Yuren and Ma, Haiching and
Peterson, Jeffrey R}]{DuongLy:2016iha}