-
1
-
-
84856694630
-
The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation
-
Lovera S, Sutto L, Boubeva R, Scapozza L, Dlker N, Gervasio FL (2012) The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation. J Am Chem Soc 134:2496–2499.
-
(2012)
J Am Chem Soc
, vol.134
, pp. 2496-2499
-
-
Lovera, S.1
Sutto, L.2
Boubeva, R.3
Scapozza, L.4
Dlker, N.5
Gervasio, F.L.6
-
2
-
-
84873135773
-
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
-
Lin YL, Meng Y, Jiang W, Roux B (2013) Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc Natl Acad Sci 110:1664–1669.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 1664-1669
-
-
Lin, Y.L.1
Meng, Y.2
Jiang, W.3
Roux, B.4
-
3
-
-
77951557992
-
Molecular dynamics simulations show that conformational selection governs the binding preferences of Imatinib for several tyrosine kinases
-
Aleksandrov A, Simonson T (2010) Molecular dynamics simulations show that conformational selection governs the binding preferences of Imatinib for several tyrosine kinases. J Biol Chem 285:13807–13815.
-
(2010)
J Biol Chem
, vol.285
, pp. 13807-13815
-
-
Aleksandrov, A.1
Simonson, T.2
-
4
-
-
0034665713
-
Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase
-
Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B, Kuriyan J (2000) Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase. Science 289:1938–1942.
-
(2000)
Science
, vol.289
, pp. 1938-1942
-
-
Schindler, T.1
Bornmann, W.2
Pellicena, P.3
Miller, W.T.4
Clarkson, B.5
Kuriyan, J.6
-
5
-
-
33847659183
-
c-Src binds to the cancer drug Imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty
-
Seeliger MA, Nagar B, Frank F, Cao X, Henderson MN, Kuriyan J (2007) c-Src binds to the cancer drug Imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty. Structure 15:299–311.
-
(2007)
Structure
, vol.15
, pp. 299-311
-
-
Seeliger, M.A.1
Nagar, B.2
Frank, F.3
Cao, X.4
Henderson, M.N.5
Kuriyan, J.6
-
6
-
-
84937110866
-
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors
-
Vijayan RSK, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL, Levy RM (2015) Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem 58:466–479.
-
(2015)
J Med Chem
, vol.58
, pp. 466-479
-
-
Vijayan, R.S.K.1
He, P.2
Modi, V.3
Duong-Ly, K.C.4
Ma, H.5
Peterson, J.R.6
Dunbrack, R.L.7
Levy, R.M.8
-
7
-
-
33745298429
-
Rational design of inhibitors that bind to inactive kinase conformations
-
Liu Y, Gray NS (2006) Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2:358–364.
-
(2006)
Nat Chem Biol
, vol.2
, pp. 358-364
-
-
Liu, Y.1
Gray, N.S.2
-
8
-
-
84941803293
-
The ABC of protein kinase conformations
-
Mbitz H (2015) The ABC of protein kinase conformations. Biochim et Biophys Acta 1854:1555–1566.
-
(2015)
Biochim et Biophys Acta
, vol.1854
, pp. 1555-1566
-
-
Mbitz, H.1
-
9
-
-
65549152514
-
Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations
-
Seeliger MA, Ranjitkar P, Kasap C, Shan Y, Shaw DE, Shah NP, Kuriyan J, Maly DJ (2009) Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations. Cancer Res 69:2384–2392.
-
(2009)
Cancer Res
, vol.69
, pp. 2384-2392
-
-
Seeliger, M.A.1
Ranjitkar, P.2
Kasap, C.3
Shan, Y.4
Shaw, D.E.5
Shah, N.P.6
Kuriyan, J.7
Maly, D.J.8
-
10
-
-
84923348238
-
Using ancient protein kinases to unravel a modern cancer drugs mechanism
-
Wilson C, Agafonov RV, Hoemberger M, Kutter S, Zorba A, Halpin J, Buosi V, Otten R, Waterman D, Theobald DL, Kern D (2015) Using ancient protein kinases to unravel a modern cancer drugs mechanism. Science 347:882–886.
-
(2015)
Science
, vol.347
, pp. 882-886
-
-
Wilson, C.1
Agafonov, R.V.2
Hoemberger, M.3
Kutter, S.4
Zorba, A.5
Halpin, J.6
Buosi, V.7
Otten, R.8
Waterman, D.9
Theobald, D.L.10
Kern, D.11
-
11
-
-
84923367313
-
Energetic dissection of Gleevec's selectivity toward human tyrosine kinases
-
Agafonov RV, Wilson C, Otten R, Buosi V, Kern D (2014) Energetic dissection of Gleevec's selectivity toward human tyrosine kinases. Nat Struct Mol Biol 21:848–853.
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 848-853
-
-
Agafonov, R.V.1
Wilson, C.2
Otten, R.3
Buosi, V.4
Kern, D.5
-
12
-
-
84875225476
-
Emerging methods in protein co-evolution
-
de Juan D, Pazos F, Valencia A (2013) Emerging methods in protein co-evolution. Nat Rev Genet 14:249–261.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 249-261
-
-
de Juan, D.1
Pazos, F.2
Valencia, A.3
-
13
-
-
84869447010
-
Protein structure prediction from sequence variation
-
Marks DS, Hopf TA, Sander C (2012) Protein structure prediction from sequence variation. Nat Biotech 30:1072–1080.
-
(2012)
Nat Biotech
, vol.30
, pp. 1072-1080
-
-
Marks, D.S.1
Hopf, T.A.2
Sander, C.3
-
14
-
-
58549114185
-
Identification of direct residue contacts in proteinprotein interaction by message passing
-
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in proteinprotein interaction by message passing. pnas 106:67–72.
-
(2009)
pnas
, vol.106
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
15
-
-
84872521100
-
Improved contact prediction in proteins: using pseudolikelihoods to infer potts models
-
Lvkvist C, Lan Y, Weigt M, Aurell E, Ekeberg M (2013) Improved contact prediction in proteins: using pseudolikelihoods to infer potts models. Phys Rev E 87:012707.
-
(2013)
Phys Rev E
, vol.87
, pp. 012707
-
-
Lvkvist, C.1
Lan, Y.2
Weigt, M.3
Aurell, E.4
Ekeberg, M.5
-
16
-
-
84890816704
-
Coevolutionary signals across protein lineages help capture multiple protein conformations
-
Morcos F, Jana B, Hwa T, Onuchic JN (2013) Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci 110:20533–20538.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 20533-20538
-
-
Morcos, F.1
Jana, B.2
Hwa, T.3
Onuchic, J.N.4
-
17
-
-
84862990368
-
Genomics-aided structure prediction
-
Sukowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN (2012) Genomics-aided structure prediction. Proc Natl Acad Sci 109:10340–10345.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 10340-10345
-
-
Sukowska, J.I.1
Morcos, F.2
Weigt, M.3
Hwa, T.4
Onuchic, J.N.5
-
18
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci 108:E1293–E1301.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. E1293-E1301
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
Zecchina, R.7
Onuchic, J.N.8
Hwa, T.9
Weigt, M.10
-
19
-
-
84941010317
-
Dimeric interactions and complex formation using direct coevolutionary couplings
-
dos Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN (2015) Dimeric interactions and complex formation using direct coevolutionary couplings. Sci Rep 5:13652.
-
(2015)
Sci Rep
, vol.5
, pp. 13652
-
-
dos Santos, R.N.1
Morcos, F.2
Jana, B.3
Andricopulo, A.D.4
Onuchic, J.N.5
-
20
-
-
82855163967
-
Protein 3D structure computed from evolutionary sequence variation
-
Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One 6:e28766EP.
-
(2011)
PLoS One
, vol.6
-
-
Marks, D.S.1
Colwell, L.J.2
Sheridan, R.3
Hopf, T.A.4
Pagnani, A.5
Zecchina, R.6
Sander, C.7
-
21
-
-
84906706579
-
Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection
-
Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG (2014) Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proc Natl Acad Sci 111:12408–12413.
-
(2014)
Proc Natl Acad Sci
, vol.111
, pp. 12408-12413
-
-
Morcos, F.1
Schafer, N.P.2
Cheng, R.R.3
Onuchic, J.N.4
Wolynes, P.G.5
-
22
-
-
84954388934
-
Constructing sequence-dependent protein models using coevolutionary information
-
Cheng RR, Raghunathan M, Noel JK, Onuchic JN (2015) Constructing sequence-dependent protein models using coevolutionary information. Prot Sci 25:111122.
-
(2015)
Prot Sci
, vol.25
, pp. 111122
-
-
Cheng, R.R.1
Raghunathan, M.2
Noel, J.K.3
Onuchic, J.N.4
-
24
-
-
70149115237
-
Constraint satisfaction problems and neural networks: a statistical physics perspective
-
Mzard M, Mora T (2009) Constraint satisfaction problems and neural networks: a statistical physics perspective. J Physiol-Paris 103:107–113.
-
(2009)
J Physiol-Paris
, vol.103
, pp. 107-113
-
-
Mzard, M.1
Mora, T.2
-
25
-
-
58549114185
-
Identification of direct residue contacts in proteinprotein interaction by message passing
-
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in proteinprotein interaction by message passing. Proc Natl Acad Sci 106:67–72.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
26
-
-
79952216403
-
Adaptive cluster expansion for inferring boltzmann machines with noisy data
-
Monasson R, Cocco S (2011) Adaptive cluster expansion for inferring boltzmann machines with noisy data. Phys Rev Lett 106:090601.
-
(2011)
Phys Rev Lett
, vol.106
, pp. 090601
-
-
Monasson, R.1
Cocco, S.2
-
27
-
-
84856090271
-
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones DT, Buchan DWA, Cozzetto D, Pontil M (2012) PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28:184–190.
-
(2012)
Bioinformatics
, vol.28
, pp. 184-190
-
-
Jones, D.T.1
Buchan, D.W.A.2
Cozzetto, D.3
Pontil, M.4
-
28
-
-
79952488320
-
Learning generative models for protein fold families
-
Balakrishnan S, Kamisetty H, Carbonell JG, Lee SI, Langmead CJ (2011) Learning generative models for protein fold families. Prot Struct, Funct, Bioinform 79:1061–1078.
-
(2011)
Prot Struct, Funct, Bioinform
, vol.79
, pp. 1061-1078
-
-
Balakrishnan, S.1
Kamisetty, H.2
Carbonell, J.G.3
Lee, S.I.4
Langmead, C.J.5
-
29
-
-
76749112068
-
Disentangling direct from indirect co-evolution of residues in protein alignments
-
Burger L, van Nimwegen E (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol 6:e1000633.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Burger, L.1
van Nimwegen, E.2
-
30
-
-
84899707813
-
Fast and accurate multivariate gaussian modeling of protein families: predicting residue contacts and protein-interaction partners
-
Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, Pagnani A (2014) Fast and accurate multivariate gaussian modeling of protein families: predicting residue contacts and protein-interaction partners. PLoS ONE 9:e92721EP.
-
(2014)
PLoS ONE
, vol.9
-
-
Baldassi, C.1
Zamparo, M.2
Feinauer, C.3
Procaccini, A.4
Zecchina, R.5
Weigt, M.6
Pagnani, A.7
-
31
-
-
84946595514
-
From residue coevolution to protein conformational ensembles and functional dynamics
-
Sutto L, Marsili S, Valencia A, Gervasio FL (2015) From residue coevolution to protein conformational ensembles and functional dynamics. Proc Natl Acad Sci 112:13567–13572.
-
(2015)
Proc Natl Acad Sci
, vol.112
, pp. 13567-13572
-
-
Sutto, L.1
Marsili, S.2
Valencia, A.3
Gervasio, F.L.4
-
32
-
-
79960975007
-
Are biological systems poised at criticality?
-
Mora T, Bialek W (2011) Are biological systems poised at criticality? J Stat Phys 144:268–302.
-
(2011)
J Stat Phys
, vol.144
, pp. 268-302
-
-
Mora, T.1
Bialek, W.2
-
33
-
-
84875546274
-
Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
-
Ferguson A, Mann J, Omarjee S, Ndungu T, Walker B, Chakraborty A (2013) Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 38:606–617.
-
(2013)
Immunity
, vol.38
, pp. 606-617
-
-
Ferguson, A.1
Mann, J.2
Omarjee, S.3
Ndungu, T.4
Walker, B.5
Chakraborty, A.6
-
34
-
-
33745283618
-
The structure of Dasatinib (BMS-0000) bound to activated ABL kinase domain elucidates its inhibitory activity against Imatinib-resistant ABL mutants
-
Tokarski JS, Newitt JA, Chang CYJ, Cheng JD, Wittekind M, Kiefer SE, Kish K, Lee FY, Borzillerri R, Lombardo LJ, Xie D, Zhang Y, Klei HE (2006) The structure of Dasatinib (BMS-0000) bound to activated ABL kinase domain elucidates its inhibitory activity against Imatinib-resistant ABL mutants. Cancer Research 66:5790–5797.
-
(2006)
Cancer Research
, vol.66
, pp. 5790-5797
-
-
Tokarski, J.S.1
Newitt, J.A.2
Cyj, C.3
Cheng, J.D.4
Wittekind, M.5
Kiefer, S.E.6
Kish, K.7
Lee, F.Y.8
Borzillerri, R.9
Lombardo, L.J.10
Xie, D.11
Zhang, Y.12
Klei, H.E.13
-
35
-
-
0036682301
-
Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and Imatinib (STI–571)
-
Nagar B, Bornmann WG, Pellicena P, Schindler T, Veach DR, Miller WT, Clarkson B, Kuriyan J (2002) Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and Imatinib (STI–571). Cancer Research 62:4236–4243.
-
(2002)
Cancer Research
, vol.62
, pp. 4236-4243
-
-
Nagar, B.1
Bornmann, W.G.2
Pellicena, P.3
Schindler, T.4
Veach, D.R.5
Miller, W.T.6
Clarkson, B.7
Kuriyan, J.8
-
36
-
-
79959758717
-
Understanding the impact of the P-loop conformation on kinase selectivity
-
Guimares CRW, Rai BK, Munchhof MJ, Liu S, Wang J, Bhattacharya SK, Buckbinder L (2011) Understanding the impact of the P-loop conformation on kinase selectivity. J Chem Inf Model 51:1199–1204.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 1199-1204
-
-
Guimares, C.R.W.1
Rai, B.K.2
Munchhof, M.J.3
Liu, S.4
Wang, J.5
Bhattacharya, S.K.6
Buckbinder, L.7
-
37
-
-
79551594605
-
Protein kinases: evolution of dynamic regulatory proteins
-
Taylor SS, Kornev AP (2011) Protein kinases: evolution of dynamic regulatory proteins. Trend Biochem Sci 36:65–77.
-
(2011)
Trend Biochem Sci
, vol.36
, pp. 65-77
-
-
Taylor, S.S.1
Kornev, A.P.2
-
38
-
-
84859961776
-
αC (alpha-C) helix as a switch in the conformational transition of Src/CDK-like kinase domains
-
Huang H, Zhao R, Dickson BM, Skeel RD, Post CB (2012) αC (alpha-C) helix as a switch in the conformational transition of Src/CDK-like kinase domains. J Phys Chem B 116:4465–4475.
-
(2012)
J Phys Chem B
, vol.116
, pp. 4465-4475
-
-
Huang, H.1
Zhao, R.2
Dickson, B.M.3
Skeel, R.D.4
Post, C.B.5
-
39
-
-
84876902448
-
Transitions to catalytically inactive conformations in EGFR kinase
-
Shan Y, Arkhipov A, Kim ET, Pan AC, Shaw DE (2013) Transitions to catalytically inactive conformations in EGFR kinase. Proc Natl Acad Sci 110:7270–7275.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 7270-7275
-
-
Shan, Y.1
Arkhipov, A.2
Kim, E.T.3
Pan, A.C.4
Shaw, D.E.5
-
40
-
-
80755125575
-
Comprehensive analysis of kinase inhibitor selectivity
-
Davis MI, Hunt JP, Herrgard S, Ciceri P, Wodicka LM, Pallares G, Hocker M, Treiber DK, Zarrinkar PP (2011) Comprehensive analysis of kinase inhibitor selectivity. Nat Biotech 29:1046–1051.
-
(2011)
Nat Biotech
, vol.29
, pp. 1046-1051
-
-
Davis, M.I.1
Hunt, J.P.2
Herrgard, S.3
Ciceri, P.4
Wodicka, L.M.5
Pallares, G.6
Hocker, M.7
Treiber, D.K.8
Zarrinkar, P.P.9
-
41
-
-
84949294800
-
Towards a molecular understanding of the link between Imatinib resistance and kinase conformational dynamics
-
Lovera S, Morando M, Pucheta-Martinez E, Martinez-Torrecuadrada JL, Saladino G, Gervasio FL (2015) Towards a molecular understanding of the link between Imatinib resistance and kinase conformational dynamics. PLoS Comput Biol 11:e1004578EP.
-
(2015)
PLoS Comput Biol
, vol.11
-
-
Lovera, S.1
Morando, M.2
Pucheta-Martinez, E.3
Martinez-Torrecuadrada, J.L.4
Saladino, G.5
Gervasio, F.L.6
-
42
-
-
84954551780
-
Aurora kinase inhibitors: current status and outlook
-
Bavetsias V, Linardopoulos S (2015) Aurora kinase inhibitors: current status and outlook. Front Oncol 5:
-
(2015)
Front Oncol
, vol.5
-
-
Bavetsias, V.1
Linardopoulos, S.2
-
43
-
-
84873721726
-
Aurora a kinase (AURKA) in normal and pathological cell division
-
Nikonova AS, Astsaturov I, Serebriiskii IG, Dunbrack RL, Golemis EA (2012) Aurora a kinase (AURKA) in normal and pathological cell division. Cell Mol Life Sci 70:661–687.
-
(2012)
Cell Mol Life Sci
, vol.70
, pp. 661-687
-
-
Nikonova, A.S.1
Astsaturov, I.2
Serebriiskii, I.G.3
Dunbrack, R.L.4
Golemis, E.A.5
-
44
-
-
31344438721
-
SAR and inhibitor complex structure determination of a novel class of potent and specific Aurora kinase inhibitors
-
Heron NM, Anderson M, Blowers DP, Breed J, Eden JM, Green S, Hill GB, Johnson T, Jung FH, McMiken HH, Mortlock AA, Pannifer AD, Pauptit RA, Pink J, Roberts NJ, Rowsell S (2006) SAR and inhibitor complex structure determination of a novel class of potent and specific Aurora kinase inhibitors. Bioorg Med Chem Lett 16:1320–1323.
-
(2006)
Bioorg Med Chem Lett
, vol.16
, pp. 1320-1323
-
-
Heron, N.M.1
Anderson, M.2
Blowers, D.P.3
Breed, J.4
Eden, J.M.5
Green, S.6
Hill, G.B.7
Johnson, T.8
Jung, F.H.9
McMiken, H.H.10
Mortlock, A.A.11
Pannifer, A.D.12
Pauptit, R.A.13
Pink, J.14
Roberts, N.J.15
Rowsell, S.16
-
45
-
-
84856489442
-
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
-
Remmert M, Biegert A, Hauser A, Soding J (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Meth 9:173–175.
-
(2012)
Nat Meth
, vol.9
, pp. 173-175
-
-
Remmert, M.1
Biegert, A.2
Hauser, A.3
Soding, J.4
-
46
-
-
84893065058
-
KLIFS: a knowledge-based structural database to navigate kinaseligand interaction space
-
van Linden OPJ, Kooistra AJ, Leurs R, de Esch IJP, de Graaf C (2014) KLIFS: a knowledge-based structural database to navigate kinaseligand interaction space. J Med Chem 57:249–277.
-
(2014)
J Med Chem
, vol.57
, pp. 249-277
-
-
van Linden, O.P.J.1
Kooistra, A.J.2
Leurs, R.3
de Esch, I.J.P.4
de Graaf, C.5
-
47
-
-
80053651587
-
Genbank
-
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) Genbank. Nucleic Acid Res 41:D36–D42.
-
(2013)
Nucleic Acid Res
, vol.41
, pp. D36-D42
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Benson, D.A.1
Cavanaugh, M.2
Clark, K.3
Karsch-Mizrachi, I.4
Lipman, D.J.5
Ostell, J.6
Sayers, E.W.7
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