-
1
-
-
33750456519
-
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
-
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, et al. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635-648.
-
(2006)
Cell
, vol.127
, pp. 635-648
-
-
Olsen, J.V.1
Blagoev, B.2
Gnad, F.3
Macek, B.4
Kumar, C.5
-
2
-
-
0037032835
-
The protein kinase complement of the human genome
-
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S, (2002) The protein kinase complement of the human genome. Science 298: 1912-1934.
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
3
-
-
0036806311
-
Evolution of protein kinase signaling from yeast to man
-
Manning G, Plowman GD, Hunter T, Sudarsanam S, (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci 27: 514-520.
-
(2002)
Trends Biochem Sci
, vol.27
, pp. 514-520
-
-
Manning, G.1
Plowman, G.D.2
Hunter, T.3
Sudarsanam, S.4
-
4
-
-
0031026008
-
The protein kinases of budding yeast: six score and more
-
Hunter T, Plowman GD, (1997) The protein kinases of budding yeast: six score and more. Trends Biochem Sci 22: 18-22.
-
(1997)
Trends Biochem Sci
, vol.22
, pp. 18-22
-
-
Hunter, T.1
Plowman, G.D.2
-
5
-
-
0029020282
-
Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification
-
Hanks SK, Hunter T, (1995) Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J 9: 576-596.
-
(1995)
FASEB J
, vol.9
, pp. 576-596
-
-
Hanks, S.K.1
Hunter, T.2
-
6
-
-
77955642537
-
Pathogenesis, classification and treatment of mastocytosis: state of the art in 2010 and future perspectives
-
Arock M, Valent P, (2010) Pathogenesis, classification and treatment of mastocytosis: state of the art in 2010 and future perspectives. Expert Rev Hematol 3: 497-516.
-
(2010)
Expert Rev Hematol
, vol.3
, pp. 497-516
-
-
Arock, M.1
Valent, P.2
-
7
-
-
0023989811
-
Primary structure of c-kit: relationship with the CSF-1/PDGF receptor kinase family-oncogenic activation of v-kit involves deletion of extracellular domain and C terminus
-
Qiu FH, Ray P, Brown K, Barker PE, Jhanwar S, et al. (1988) Primary structure of c-kit: relationship with the CSF-1/PDGF receptor kinase family-oncogenic activation of v-kit involves deletion of extracellular domain and C terminus. EMBO J 7: 1003-1011.
-
(1988)
EMBO J
, vol.7
, pp. 1003-1011
-
-
Qiu, F.H.1
Ray, P.2
Brown, K.3
Barker, P.E.4
Jhanwar, S.5
-
8
-
-
77953896432
-
Cell Signaling by Receptor Tyrosine Kinases
-
Lemmon MA, Schlessinger J, (2010) Cell Signaling by Receptor Tyrosine Kinases. Cell 141: 1117-1134.
-
(2010)
Cell
, vol.141
, pp. 1117-1134
-
-
Lemmon, M.A.1
Schlessinger, J.2
-
9
-
-
2742529418
-
Human Protooncogene C-Kit - A New Cell-Surface Receptor Tyrosine Kinase for An Unidentified Ligand
-
Yarden Y, Kuang WJ, Yangfeng T, Coussens L, Munemitsu S, et al. (1987) Human Protooncogene C-Kit- A New Cell-Surface Receptor Tyrosine Kinase for An Unidentified Ligand. EMBO J 6: 3341-3351.
-
(1987)
EMBO J
, vol.6
, pp. 3341-3351
-
-
Yarden, Y.1
Kuang, W.J.2
Yangfeng, T.3
Coussens, L.4
Munemitsu, S.5
-
10
-
-
34548501985
-
c-Kit-a hematopoietic cell essential receptor tyrosine kinase
-
Edling CE, Hallberg B, (2007) c-Kit-a hematopoietic cell essential receptor tyrosine kinase. Int J Biochem Cell Biol 39: 1995-1998.
-
(2007)
Int J Biochem Cell Biol
, vol.39
, pp. 1995-1998
-
-
Edling, C.E.1
Hallberg, B.2
-
11
-
-
27744551009
-
Structure and regulation of Kit protein-tyrosine kinase - The stem cell factor receptor
-
Roskoski R, (2005) Structure and regulation of Kit protein-tyrosine kinase- The stem cell factor receptor. Bioch Biophys Res Commun 338: 1307-1315.
-
(2005)
Bioch Biophys Res Commun
, vol.338
, pp. 1307-1315
-
-
Roskoski, R.1
-
12
-
-
0029785474
-
The kinase insert domain of interferon-induced protein kinase PKR is required for activity but not for interaction with the pseudosubstrate K3L
-
Craig AWB, Cosentino GP, Donze O, Sonenberg N, (1996) The kinase insert domain of interferon-induced protein kinase PKR is required for activity but not for interaction with the pseudosubstrate K3L. J Biol Chem 271: 24526-24533.
-
(1996)
J Biol Chem
, vol.271
, pp. 24526-24533
-
-
Craig, A.W.B.1
Cosentino, G.P.2
Donze, O.3
Sonenberg, N.4
-
13
-
-
0025343230
-
Signal transduction by receptors with tyrosine kinase activity
-
Ullrich A, Schlessinger J, (1990) Signal transduction by receptors with tyrosine kinase activity. Cell 61: 203-212.
-
(1990)
Cell
, vol.61
, pp. 203-212
-
-
Ullrich, A.1
Schlessinger, J.2
-
14
-
-
33846987130
-
Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases
-
Liu H, Chen X, Focia PJ, He X, (2007) Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases. EMBO J 26: 891-901.
-
(2007)
EMBO J
, vol.26
, pp. 891-901
-
-
Liu, H.1
Chen, X.2
Focia, P.J.3
He, X.4
-
15
-
-
34447531743
-
Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor
-
Yuzawa S, Opatowsky Y, Zhang Z, Mandiyan V, Lax I, et al. (2007) Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor. Cell 130: 323-334.
-
(2007)
Cell
, vol.130
, pp. 323-334
-
-
Yuzawa, S.1
Opatowsky, Y.2
Zhang, Z.3
Mandiyan, V.4
Lax, I.5
-
16
-
-
0032493859
-
Switching signals on or off by receptor dimerization
-
Weiss A, Schlessinger J, (1998) Switching signals on or off by receptor dimerization. Cell 94: 277-280.
-
(1998)
Cell
, vol.94
, pp. 277-280
-
-
Weiss, A.1
Schlessinger, J.2
-
17
-
-
0034644539
-
Cell signaling by receptor tyrosine kinases
-
Schlessinger J, (2000) Cell signaling by receptor tyrosine kinases. Cell 103: 211-225.
-
(2000)
Cell
, vol.103
, pp. 211-225
-
-
Schlessinger, J.1
-
18
-
-
0032857449
-
The biology of stem cell factor and its receptor C-kit
-
Ashman LK, (1999) The biology of stem cell factor and its receptor C-kit. International J Biochem Cell Biol 31: 1037-1051.
-
(1999)
International J Biochem Cell Biol
, vol.31
, pp. 1037-1051
-
-
Ashman, L.K.1
-
19
-
-
0037013143
-
The conformational plasticity of protein kinases
-
Huse M, Kuriyan J, (2002) The conformational plasticity of protein kinases. Cell 109: 275-282.
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
20
-
-
4444353636
-
Regulation of protein kinases; controlling activity through activation segment conformation
-
Nolen B, Taylor S, Ghosh G, (2004) Regulation of protein kinases; controlling activity through activation segment conformation. Mol Cell 15: 661-675.
-
(2004)
Mol Cell
, vol.15
, pp. 661-675
-
-
Nolen, B.1
Taylor, S.2
Ghosh, G.3
-
21
-
-
0842310394
-
The structural basis for autoinhibition of FLT3 by the juxtamembrane domain
-
Griffith J, Black J, Faerman C, Swenson L, Wynn M, et al. (2004) The structural basis for autoinhibition of FLT3 by the juxtamembrane domain. Mol Cell 13: 169-178.
-
(2004)
Mol Cell
, vol.13
, pp. 169-178
-
-
Griffith, J.1
Black, J.2
Faerman, C.3
Swenson, L.4
Wynn, M.5
-
22
-
-
0034614490
-
Signaling - 2000 and beyond
-
Hunter T, (2000) Signaling- 2000 and beyond. Cell 100: 113-127.
-
(2000)
Cell
, vol.100
, pp. 113-127
-
-
Hunter, T.1
-
23
-
-
0028838971
-
Protein-Kinases and Phosphatases - the Yin and Yang of Protein-Phosphorylation and Signaling
-
Hunter T, (1995) Protein-Kinases and Phosphatases- the Yin and Yang of Protein-Phosphorylation and Signaling. Cell 80: 225-236.
-
(1995)
Cell
, vol.80
, pp. 225-236
-
-
Hunter, T.1
-
24
-
-
0028796630
-
W/Kit Gene Required for Interstitial-Cells of Cajal and for Intestinal Pacemaker Activity
-
Huizinga JD, Thuneberg L, Kluppel M, Malysz J, Mikkelsen HB, et al. (1995) W/Kit Gene Required for Interstitial-Cells of Cajal and for Intestinal Pacemaker Activity. Nature 373: 347-349.
-
(1995)
Nature
, vol.373
, pp. 347-349
-
-
Huizinga, J.D.1
Thuneberg, L.2
Kluppel, M.3
Malysz, J.4
Mikkelsen, H.B.5
-
25
-
-
0018344526
-
Decreased Production of Mast-Cells in S1-S1D Anemic Mice
-
Kitamura Y, Go S, (1979) Decreased Production of Mast-Cells in S1-S1D Anemic Mice. Blood 53: 492-497.
-
(1979)
Blood
, vol.53
, pp. 492-497
-
-
Kitamura, Y.1
Go, S.2
-
26
-
-
0018596155
-
Distribution of Mast-Cell Precursors in Hematopoietic and Lymphopoietic Tissues of Mice
-
Kitamura Y, Shimada M, Go S, Matsuda H, Hatanaka K, et al. (1979) Distribution of Mast-Cell Precursors in Hematopoietic and Lymphopoietic Tissues of Mice. J Exp Med 150: 482-490.
-
(1979)
J Exp Med
, vol.150
, pp. 482-490
-
-
Kitamura, Y.1
Shimada, M.2
Go, S.3
Matsuda, H.4
Hatanaka, K.5
-
27
-
-
0018096538
-
Decrease of Mast-Cells in W-W Nu Mice and Their Increase by Bone-Marrow Transplantation
-
Kitamura Y, Go S, Hatanaka K, (1978) Decrease of Mast-Cells in W-W Nu Mice and Their Increase by Bone-Marrow Transplantation. Blood 52: 447-452.
-
(1978)
Blood
, vol.52
, pp. 447-452
-
-
Kitamura, Y.1
Go, S.2
Hatanaka, K.3
-
28
-
-
12144278434
-
Normal and oncogenic forms of the receptor tyrosine kinase kit
-
Lennartsson J, Jelacic T, Linnekin D, Shivakrupa R, (2005) Normal and oncogenic forms of the receptor tyrosine kinase kit. Stem Cells 23: 16-43.
-
(2005)
Stem Cells
, vol.23
, pp. 16-43
-
-
Lennartsson, J.1
Jelacic, T.2
Linnekin, D.3
Shivakrupa, R.4
-
29
-
-
12144257058
-
Kit as a human oncogenic tyrosine kinase
-
Kitamura Y, Hirotab S, (2004) Kit as a human oncogenic tyrosine kinase. Cell Mol Life Sci 61: 2924-2931.
-
(2004)
Cell Mol Life Sci
, vol.61
, pp. 2924-2931
-
-
Kitamura, Y.1
Hirotab, S.2
-
30
-
-
0036769966
-
Pathology and diagnostic criteria of gastrointestinal stromal tumors (GISTs): a review
-
Miettinen M, Majidi M, Lasota J, (2002) Pathology and diagnostic criteria of gastrointestinal stromal tumors (GISTs): a review. Eur J Cancer 38: S39-S51.
-
(2002)
Eur J Cancer
, vol.38
, pp. 39-51
-
-
Miettinen, M.1
Majidi, M.2
Lasota, J.3
-
31
-
-
0141836914
-
FLT3: ITDoes matter in leukemia
-
Levis M, Small D, (2003) FLT3: ITDoes matter in leukemia. Leukemia 17: 1738-1752.
-
(2003)
Leukemia
, vol.17
, pp. 1738-1752
-
-
Levis, M.1
Small, D.2
-
32
-
-
0027359443
-
Identification of Mutations in the Coding Sequence of the Protooncogene C-Kit in A Human Mast-Cell Leukemia-Cell Line Causing Ligand-Independent Activation of C-Kit Product
-
Furitsu T, Tsujimura T, Tono T, Ikeda H, Kitayama H, et al. (1993) Identification of Mutations in the Coding Sequence of the Protooncogene C-Kit in A Human Mast-Cell Leukemia-Cell Line Causing Ligand-Independent Activation of C-Kit Product. J Clin Invest 92: 1736-1744.
-
(1993)
J Clin Invest
, vol.92
, pp. 1736-1744
-
-
Furitsu, T.1
Tsujimura, T.2
Tono, T.3
Ikeda, H.4
Kitayama, H.5
-
33
-
-
0032873349
-
KIT protein expression and analysis of c-kit gene mutation in adenoid cystic carcinoma
-
Holst VA, Marshall CE, Moskaluk CA, Frierson HF, (1999) KIT protein expression and analysis of c-kit gene mutation in adenoid cystic carcinoma. Mod Pathol 12: 956-960.
-
(1999)
Mod Pathol
, vol.12
, pp. 956-960
-
-
Holst, V.A.1
Marshall, C.E.2
Moskaluk, C.A.3
Frierson, H.F.4
-
34
-
-
31444451841
-
Cosmic 2005
-
Forbes S, Clements J, Dawson E, Bamford S, Webb T, et al. (2006) Cosmic 2005. Br J Cancer 94: 318-322.
-
(2006)
Br J Cancer
, vol.94
, pp. 318-322
-
-
Forbes, S.1
Clements, J.2
Dawson, E.3
Bamford, S.4
Webb, T.5
-
35
-
-
67649950344
-
Mechanisms of secondary resistance to tyrosine kinase inhibitors in gastrointestinal stromal tumours (Review)
-
Maleddu A, Pantaleo MA, Nannini M, Di BM, Saponara M, et al. (2009) Mechanisms of secondary resistance to tyrosine kinase inhibitors in gastrointestinal stromal tumours (Review). Oncol Rep 21: 1359-1366.
-
(2009)
Oncol Rep
, vol.21
, pp. 1359-1366
-
-
Maleddu, A.1
Pantaleo, M.A.2
Nannini, M.3
Di, B.M.4
Saponara, M.5
-
36
-
-
0034993741
-
Classes of c-KIT activating mutations: proposed mechanisms of action and implications for disease classification and therapy
-
Longley BJ, Reguera MJ, Ma Y, (2001) Classes of c-KIT activating mutations: proposed mechanisms of action and implications for disease classification and therapy. Leuk Res 25: 571-576.
-
(2001)
Leuk Res
, vol.25
, pp. 571-576
-
-
Longley, B.J.1
Reguera, M.J.2
Ma, Y.3
-
37
-
-
0035320853
-
Gastrointestinal stromal tumor with a novel mutation of KIT proto-oncogene
-
Fukuda R, Hamamoto N, Uchida Y, Furuta K, Katsube T, et al. (2001) Gastrointestinal stromal tumor with a novel mutation of KIT proto-oncogene. Int Med 40: 301-303.
-
(2001)
Int Med
, vol.40
, pp. 301-303
-
-
Fukuda, R.1
Hamamoto, N.2
Uchida, Y.3
Furuta, K.4
Katsube, T.5
-
38
-
-
0028959163
-
Constitutively activating mutations of c-kit receptor tyrosine kinase confer factor-independent growth and tumorigenicity of factor-dependent hematopoietic cell lines
-
Kitayama H, Kanakura Y, Furitsu T, Tsujimura T, Oritani K, et al. (1995) Constitutively activating mutations of c-kit receptor tyrosine kinase confer factor-independent growth and tumorigenicity of factor-dependent hematopoietic cell lines. Blood 85: 790-798.
-
(1995)
Blood
, vol.85
, pp. 790-798
-
-
Kitayama, H.1
Kanakura, Y.2
Furitsu, T.3
Tsujimura, T.4
Oritani, K.5
-
39
-
-
0035871889
-
Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies
-
Yamamoto Y, Kiyoi H, Nakano Y, Suzuki R, Kodera Y, et al. (2001) Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies. Blood 97: 2434-2439.
-
(2001)
Blood
, vol.97
, pp. 2434-2439
-
-
Yamamoto, Y.1
Kiyoi, H.2
Nakano, Y.3
Suzuki, R.4
Kodera, Y.5
-
40
-
-
0042357240
-
Structure of a c-kit product complex reveals the basis for kinase transactivation
-
Mol CD, Lim KB, Sridhar V, Zou H, Chien EY, et al. (2003) Structure of a c-kit product complex reveals the basis for kinase transactivation. J Biol Chem 278: 31461-31464.
-
(2003)
J Biol Chem
, vol.278
, pp. 31461-31464
-
-
Mol, C.D.1
Lim, K.B.2
Sridhar, V.3
Zou, H.4
Chien, E.Y.5
-
41
-
-
4444311694
-
Analysis of the activating mutations within the activation loop of leukemia targets Flt-3 and c-Kit based on protein homology modeling
-
Torrent M, Rickert K, Pan BS, Sepp-Lorenzino L, (2004) Analysis of the activating mutations within the activation loop of leukemia targets Flt-3 and c-Kit based on protein homology modeling. J Mol Graph Model 23: 153-165.
-
(2004)
J Mol Graph Model
, vol.23
, pp. 153-165
-
-
Torrent, M.1
Rickert, K.2
Pan, B.S.3
Sepp-Lorenzino, L.4
-
42
-
-
0035469886
-
Phosphatidylinositol 3 kinase contributes to the transformation of hematopoietic cells by the D816V c-Kit mutant
-
Chian RJ, Young S, Danilkovitch-Miagkova A, Ronnstrand L, Leonard E, et al. (2001) Phosphatidylinositol 3 kinase contributes to the transformation of hematopoietic cells by the D816V c-Kit mutant. Blood 98: 1365-1373.
-
(2001)
Blood
, vol.98
, pp. 1365-1373
-
-
Chian, R.J.1
Young, S.2
Danilkovitch-Miagkova, A.3
Ronnstrand, L.4
Leonard, E.5
-
43
-
-
70349507344
-
The aberrant localization of oncogenic kit tyrosine kinase receptor mutants is reversed on specific inhibitory treatment
-
Bougherara H, Subra F, Crepin R, Tauc P, Auclair C, et al. (2009) The aberrant localization of oncogenic kit tyrosine kinase receptor mutants is reversed on specific inhibitory treatment. Mol Cancer Res 7: 1525-1533.
-
(2009)
Mol Cancer Res
, vol.7
, pp. 1525-1533
-
-
Bougherara, H.1
Subra, F.2
Crepin, R.3
Tauc, P.4
Auclair, C.5
-
44
-
-
0033557589
-
Activating mutation in the catalytic domain of c-kit elicits hematopoietic transformation by receptor self-association not at the ligand-induced dimerization site
-
Tsujimura T, Hashimoto K, Kitayama H, Ikeda H, Sugahara H, et al. (1999) Activating mutation in the catalytic domain of c-kit elicits hematopoietic transformation by receptor self-association not at the ligand-induced dimerization site. Blood 93: 1319-1329.
-
(1999)
Blood
, vol.93
, pp. 1319-1329
-
-
Tsujimura, T.1
Hashimoto, K.2
Kitayama, H.3
Ikeda, H.4
Sugahara, H.5
-
45
-
-
23644452511
-
Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?
-
Kannan N, Neuwald AF, (2005) Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? J Mol Biol 351: 956-972.
-
(2005)
J Mol Biol
, vol.351
, pp. 956-972
-
-
Kannan, N.1
Neuwald, A.F.2
-
47
-
-
77951270272
-
Large conformational changes in proteins: signaling and other functions
-
Grant BJ, Gorfe AA, McCammon JA, (2010) Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol 20: 142-147.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 142-147
-
-
Grant, B.J.1
Gorfe, A.A.2
McCammon, J.A.3
-
48
-
-
77954913405
-
Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor
-
Laine E, Goncalves C, Karst JC, Lesnard A, Rault S, et al. (2010) Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor. Proc Natl Acad Sci U S A 107: 11277-11282.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 11277-11282
-
-
Laine, E.1
Goncalves, C.2
Karst, J.C.3
Lesnard, A.4
Rault, S.5
-
49
-
-
64849113665
-
Trapping moving targets with small molecules
-
Lee GM, Craik CS, (2009) Trapping moving targets with small molecules. Science 324: 213-215.
-
(2009)
Science
, vol.324
, pp. 213-215
-
-
Lee, G.M.1
Craik, C.S.2
-
50
-
-
27644462900
-
The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation
-
Banavali NK, Roux B, (2005) The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure 13: 1715-1723.
-
(2005)
Structure
, vol.13
, pp. 1715-1723
-
-
Banavali, N.K.1
Roux, B.2
-
51
-
-
34248532092
-
Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck
-
Banavali NK, Roux B, (2007) Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins 67: 1096-1112.
-
(2007)
Proteins
, vol.67
, pp. 1096-1112
-
-
Banavali, N.K.1
Roux, B.2
-
52
-
-
59449100832
-
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
-
Banavali NK, Roux B, (2009) Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins 74: 378-389.
-
(2009)
Proteins
, vol.74
, pp. 378-389
-
-
Banavali, N.K.1
Roux, B.2
-
53
-
-
67649781716
-
Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics
-
Kastner J, Loeffler HH, Roberts SK, Martin-Fernandez ML, Winn MD, (2009) Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics. J Struct Biol 167: 117-128.
-
(2009)
J Struct Biol
, vol.167
, pp. 117-128
-
-
Kastner, J.1
Loeffler, H.H.2
Roberts, S.K.3
Martin-Fernandez, M.L.4
Winn, M.D.5
-
54
-
-
69049106642
-
New insights into the activation of Escherichia coli tyrosine kinase revealed by molecular dynamics simulation and biochemical analysis
-
Lu T, Tan H, Lee D, Chen G, Jia Z, (2009) New insights into the activation of Escherichia coli tyrosine kinase revealed by molecular dynamics simulation and biochemical analysis. Biochemistry 48: 7986-7995.
-
(2009)
Biochemistry
, vol.48
, pp. 7986-7995
-
-
Lu, T.1
Tan, H.2
Lee, D.3
Chen, G.4
Jia, Z.5
-
55
-
-
70149117469
-
Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
-
Dixit A, Verkhivker GM, (2009) Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations. PLoS Comput Biol 5: e1000487.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Dixit, A.1
Verkhivker, G.M.2
-
56
-
-
61549094352
-
Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability
-
Dixit A, Torkamani A, Schork NJ, Verkhivker G, (2009) Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability. Biophys J 96: 858-874.
-
(2009)
Biophys J
, vol.96
, pp. 858-874
-
-
Dixit, A.1
Torkamani, A.2
Schork, N.J.3
Verkhivker, G.4
-
57
-
-
33749002274
-
Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations
-
Liu B, Bernard B, Wu JH, (2006) Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations. Proteins 65: 331-346.
-
(2006)
Proteins
, vol.65
, pp. 331-346
-
-
Liu, B.1
Bernard, B.2
Wu, J.H.3
-
58
-
-
70149090164
-
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
-
Bakan A, Bahar I, (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A 106: 14349-14354.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
59
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto CN, Kovacs JA, Abagyan RA, (2005) Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 127: 9632-9640.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
60
-
-
45749139232
-
Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking
-
May A, Zacharias M, (2008) Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. J Med Chem 51: 3499-3506.
-
(2008)
J Med Chem
, vol.51
, pp. 3499-3506
-
-
May, A.1
Zacharias, M.2
-
61
-
-
30044434744
-
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
-
Tobi D, Bahar I, (2005) Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci U S A 102: 18908-18913.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
62
-
-
77957241496
-
Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation
-
Cheng S, Niv MY, (2010) Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. J Chem Inf Model 50: 1602-1610.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1602-1610
-
-
Cheng, S.1
Niv, M.Y.2
-
63
-
-
26444598487
-
Molecular modeling of wild-type and D816V c-kit inhibition based on ATP-competitive binding of ellipticine derivatives to tyrosine kinases
-
Vendome J, Letard S, Martin F, Svinarchuk F, Dubreuil P, et al. (2005) Molecular modeling of wild-type and D816V c-kit inhibition based on ATP-competitive binding of ellipticine derivatives to tyrosine kinases. J Med Chem 48: 6194-6201.
-
(2005)
J Med Chem
, vol.48
, pp. 6194-6201
-
-
Vendome, J.1
Letard, S.2
Martin, F.3
Svinarchuk, F.4
Dubreuil, P.5
-
64
-
-
4444230149
-
Molecular basis of the constitutive activity and STI571 resistance of Asp816Val mutant KIT receptor tyrosine kinase
-
Foster R, Griffith R, Ferrao P, Ashman L, (2004) Molecular basis of the constitutive activity and STI571 resistance of Asp816Val mutant KIT receptor tyrosine kinase. J Mol Graph Model 23: 139-152.
-
(2004)
J Mol Graph Model
, vol.23
, pp. 139-152
-
-
Foster, R.1
Griffith, R.2
Ferrao, P.3
Ashman, L.4
-
65
-
-
46449120133
-
Induced disorder in protein-ligand complexes as a drug-design strategy
-
Crespo A, Fernandez A, (2008) Induced disorder in protein-ligand complexes as a drug-design strategy. Mol Pharm 5: 430-437.
-
(2008)
Mol Pharm
, vol.5
, pp. 430-437
-
-
Crespo, A.1
Fernandez, A.2
-
66
-
-
34249290776
-
Rational drug redesign to overcome drug resistance in cancer therapy: imatinib moving target
-
Fernandez A, Sanguino A, Peng Z, Crespo A, Ozturk E, et al. (2007) Rational drug redesign to overcome drug resistance in cancer therapy: imatinib moving target. Cancer Res 67: 4028-4033.
-
(2007)
Cancer Res
, vol.67
, pp. 4028-4033
-
-
Fernandez, A.1
Sanguino, A.2
Peng, Z.3
Crespo, A.4
Ozturk, E.5
-
67
-
-
60849113175
-
KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients
-
Gajiwala KS, Wu JC, Christensen J, Deshmukh GD, Diehl W, et al. (2009) KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Proc Natl Acad Sci U S A 106: 1542-1547.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 1542-1547
-
-
Gajiwala, K.S.1
Wu, J.C.2
Christensen, J.3
Deshmukh, G.D.4
Diehl, W.5
-
68
-
-
44949190466
-
Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process
-
Zou J, Wang YD, Ma FX, Xiang ML, Shi B, et al. (2008) Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process. Proteins 72: 323-332.
-
(2008)
Proteins
, vol.72
, pp. 323-332
-
-
Zou, J.1
Wang, Y.D.2
Ma, F.X.3
Xiang, M.L.4
Shi, B.5
-
69
-
-
2942542387
-
Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase
-
Mol CD, Dougan DR, Schneider TR, Skene RJ, Kraus ML, et al. (2004) Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J Biol Chem 279: 31655-31663.
-
(2004)
J Biol Chem
, vol.279
, pp. 31655-31663
-
-
Mol, C.D.1
Dougan, D.R.2
Schneider, T.R.3
Skene, R.J.4
Kraus, M.L.5
-
70
-
-
77950617070
-
Function of activation loop tyrosine phosphorylation in the mechanism of c-Kit auto-activation and its implication in sunitinib resistance
-
DiNitto JP, Deshmukh GD, Zhang Y, Jacques SL, Coli R, et al. (2010) Function of activation loop tyrosine phosphorylation in the mechanism of c-Kit auto-activation and its implication in sunitinib resistance. J Biochem 147: 601-609.
-
(2010)
J Biochem
, vol.147
, pp. 601-609
-
-
DiNitto, J.P.1
Deshmukh, G.D.2
Zhang, Y.3
Jacques, S.L.4
Coli, R.5
-
71
-
-
33745759471
-
Ensemble-based convergence analysis of biomolecular trajectories
-
Lyman E, Zuckerman DM, (2006) Ensemble-based convergence analysis of biomolecular trajectories. Biophys J 91: 164-172.
-
(2006)
Biophys J
, vol.91
, pp. 164-172
-
-
Lyman, E.1
Zuckerman, D.M.2
-
72
-
-
44349088854
-
The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis
-
Laine E, Yoneda JD, Blondel A, Malliavin TE, (2008) The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis. Proteins 71: 1813-1829.
-
(2008)
Proteins
, vol.71
, pp. 1813-1829
-
-
Laine, E.1
Yoneda, J.D.2
Blondel, A.3
Malliavin, T.E.4
-
73
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, et al. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.H.5
-
74
-
-
0002611483
-
Estimation of statistical errors in molecular simulation calculations
-
Straatsma TP, Berendsen HJC, Stam AJ, (1986) Estimation of statistical errors in molecular simulation calculations. Mol Phys 57: 89-95.
-
(1986)
Mol Phys
, vol.57
, pp. 89-95
-
-
Straatsma, T.P.1
Berendsen, H.J.C.2
Stam, A.J.3
-
75
-
-
2342648012
-
Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions
-
Blondel A, (2004) Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions. J Comput Chem 25: 985-993.
-
(2004)
J Comput Chem
, vol.25
, pp. 985-993
-
-
Blondel, A.1
-
76
-
-
77958451570
-
Activation of the edema factor of Bacillus anthracis by Calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding
-
Laine E, Martinez L, Blondel A, Malliavin TE, (2010) Activation of the edema factor of Bacillus anthracis by Calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding. Biophys J 99: 2264-2272.
-
(2010)
Biophys J
, vol.99
, pp. 2264-2272
-
-
Laine, E.1
Martinez, L.2
Blondel, A.3
Malliavin, T.E.4
-
77
-
-
49649108911
-
Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib
-
Vajpai N, Strauss A, Fendrich G, Cowan-Jacob SW, Manley PW, et al. (2008) Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. J Biol Chem 283: 18292-18302.
-
(2008)
J Biol Chem
, vol.283
, pp. 18292-18302
-
-
Vajpai, N.1
Strauss, A.2
Fendrich, G.3
Cowan-Jacob, S.W.4
Manley, P.W.5
-
78
-
-
77949382914
-
Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease
-
Batista PR, Robert CH, Marechal JD, Hamida-Rebai MB, Pascutti PG, et al. (2010) Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease. Phys Chem Chem Phys 12: 2850-2859.
-
(2010)
Phys Chem Chem Phys
, vol.12
, pp. 2850-2859
-
-
Batista, P.R.1
Robert, C.H.2
Marechal, J.D.3
Hamida-Rebai, M.B.4
Pascutti, P.G.5
-
79
-
-
70449379413
-
Sequence and structure signatures of cancer mutation hotspots in protein kinases
-
Dixit A, Yi L, Gowthaman R, Torkamani A, Schork NJ, et al. (2009) Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS One 4: e7485.
-
(2009)
PLoS One
, vol.4
-
-
Dixit, A.1
Yi, L.2
Gowthaman, R.3
Torkamani, A.4
Schork, N.J.5
-
80
-
-
67049154293
-
The crystal structure of BRAF in complex with an organoruthenium inhibitor reveals a mechanism for inhibition of an active form of BRAF kinase
-
Xie P, Streu C, Qin J, Bregman H, Pagano N, et al. (2009) The crystal structure of BRAF in complex with an organoruthenium inhibitor reveals a mechanism for inhibition of an active form of BRAF kinase. Biochemistry 48: 5187-5198.
-
(2009)
Biochemistry
, vol.48
, pp. 5187-5198
-
-
Xie, P.1
Streu, C.2
Qin, J.3
Bregman, H.4
Pagano, N.5
-
81
-
-
78349232462
-
Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases
-
Bae JH, Schlessinger J, (2010) Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases. Mol Cells 29: 443-448.
-
(2010)
Mol Cells
, vol.29
, pp. 443-448
-
-
Bae, J.H.1
Schlessinger, J.2
-
82
-
-
77649251478
-
Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells
-
Bae JH, Boggon TJ, Tome F, Mandiyan V, Lax I, et al. (2010) Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells. Proc Natl Acad Sci U S A 107: 2866-2871.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 2866-2871
-
-
Bae, J.H.1
Boggon, T.J.2
Tome, F.3
Mandiyan, V.4
Lax, I.5
-
83
-
-
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
-
84
-
-
0020997912
-
Dictionary of Protein Secondary Structure - Pattern-Recognition of Hydrogen-Bonded and Geometrical Features
-
Kabsch W, Sander C, (1983) Dictionary of Protein Secondary Structure- Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
85
-
-
0034663597
-
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
-
Cuff JA, Barton GJ, (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins Struct Funct Genet 40: 502-511.
-
(2000)
Proteins Struct Funct Genet
, vol.40
, pp. 502-511
-
-
Cuff, J.A.1
Barton, G.J.2
-
86
-
-
0028304962
-
Satisfying Hydrogen-Bonding Potential in Proteins
-
Mcdonald IK, Thornton JM, (1994) Satisfying Hydrogen-Bonding Potential in Proteins. J Mol Biol 238: 777-793.
-
(1994)
J Mol Biol
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
87
-
-
79959855072
-
-
The PyMOL Molecular Grapics System, Delano Scientific, San Carlos, CA, USA
-
DeLano WL, (2002) The PyMOL Molecular Grapics System, Delano Scientific, San Carlos, CA, USA.
-
(2002)
-
-
DeLano, W.L.1
-
88
-
-
0026696669
-
Definition and Display of Steric, Hydrophobic, and Hydrogen-Bonding Properties of Ligand-Binding Sites in Proteins Using Lee and Richards Accessible Surface - Validation of A High-Resolution Graphical Tool for Drug Design
-
Bohacek RS, Mcmartin C, (1992) Definition and Display of Steric, Hydrophobic, and Hydrogen-Bonding Properties of Ligand-Binding Sites in Proteins Using Lee and Richards Accessible Surface- Validation of A High-Resolution Graphical Tool for Drug Design. J Med Chem 35: 1671-1684.
-
(1992)
J Med Chem
, vol.35
, pp. 1671-1684
-
-
Bohacek, R.S.1
McMartin, C.2
-
89
-
-
0346458811
-
N - H...O, O - H...O, and C - H...O hydrogen bonds in protein-ligand complexes: Strong and weak interactions in molecular recognition
-
Sarkhel S, Desiraju GR, (2004) N- H...O, O- H...O, and C- H...O hydrogen bonds in protein-ligand complexes: Strong and weak interactions in molecular recognition. Proteins Struct Funct Genet 54: 247-259.
-
(2004)
Proteins Struct Funct Genet
, vol.54
, pp. 247-259
-
-
Sarkhel, S.1
Desiraju, G.R.2
-
90
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucl Acids Res 28: 235-242.
-
(2000)
Nucl Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
91
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser A, Do RKG, Sali A, (2000) Modeling of loops in protein structures. Protein Science 9: 1753-1773.
-
(2000)
Protein Science
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.G.2
Sali, A.3
-
92
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, et al. (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29: 291-325.
-
(2000)
Annu Rev Biophys Biomol Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
-
93
-
-
0242443693
-
Force fields for protein simulations
-
Ponder JW, Case DA, (2003) Force fields for protein simulations. Adv Protein Chem 66: 27-85.
-
(2003)
Adv Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
94
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
-
95
-
-
0000035913
-
Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density
-
Jorgensen WL, Jenson C, (1998) Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density. J Comput Chem 19: 1179-1186.
-
(1998)
J Comput Chem
, vol.19
, pp. 1179-1186
-
-
Jorgensen, W.L.1
Jenson, C.2
-
96
-
-
33750587438
-
Molecular-Dynamics with Coupling to An External Bath
-
Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR, (1984) Molecular-Dynamics with Coupling to An External Bath. J Chem Phys 81: 3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
97
-
-
0026869597
-
Langevin Dynamics of Peptides - the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N'-Methylamide
-
Loncharich RJ, Brooks BR, Pastor RW, (1992) Langevin Dynamics of Peptides- the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N'-Methylamide. Biopolymers 32: 523-535.
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
98
-
-
33846823909
-
Particle Mesh Ewald - An N.Log(N) Method for Ewald Sums in Large Systems
-
Darden T, York D, Pedersen L, (1993) Particle Mesh Ewald- An N.Log(N) Method for Ewald Sums in Large Systems. J Chem Phys 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
99
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner MF, Olson AJ, Spehner JC, (1996) Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38: 305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
100
-
-
0028922586
-
Ligplot - A Program to Generate Schematic Diagrams of Protein Ligand Interactions
-
Wallace AC, Laskowski RA, Thornton JM, (1995) Ligplot- A Program to Generate Schematic Diagrams of Protein Ligand Interactions. Protein Eng 8: 127-134.
-
(1995)
Protein Eng
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
102
-
-
35148855766
-
Lexical scope and statistical computing
-
Gentleman R, Ihaka R, (2000) Lexical scope and statistical computing. J Comput Graph Stat 9: 491-508.
-
(2000)
J Comput Graph Stat
, vol.9
, pp. 491-508
-
-
Gentleman, R.1
Ihaka, R.2
-
103
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
Bashford D, Case DA, (2000) Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem 51: 129-152.
-
(2000)
Annu Rev Phys Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
104
-
-
20644449471
-
Modification of the generalized Born model suitable for macromolecules
-
Onufriev A, Bashford D, Case DA, (2000) Modification of the generalized Born model suitable for macromolecules. J Phys Chem B 104: 3712-3720.
-
(2000)
J Phys Chem B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
105
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
DOI 10.1002/prot.20033
-
Onufriev A, Bashford D, Case DA, (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55: 383-394 DOI 10.1002/prot.20033.
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
106
-
-
0029374782
-
Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin
-
Perahia D, Mouawad L, (1995) Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. J Comput Chem 19: 241-246.
-
(1995)
J Comput Chem
, vol.19
, pp. 241-246
-
-
Perahia, D.1
Mouawad, L.2
-
107
-
-
84986512474
-
Charmm - A Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) Charmm- A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J Comput Chem 4: 187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
-
108
-
-
67650500988
-
CHARMM: The Biomolecular Simulation Program
-
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, et al. (2009) CHARMM: The Biomolecular Simulation Program. J Comput Chem 30: 1545-1614.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
Mackerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
-
109
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand YH, (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14: 1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
110
-
-
0000216012
-
Collective Protein Dynamics and Nuclear-Spin Relaxation
-
Bruschweiler R, (1995) Collective Protein Dynamics and Nuclear-Spin Relaxation. J Chem Phys 102: 3396-3403.
-
(1995)
J Chem Phys
, vol.102
, pp. 3396-3403
-
-
Bruschweiler, R.1
-
111
-
-
33748759844
-
Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors
-
Floquet N, Marechal JD, Badet-Denisot MA, Robert CH, Dauchez M, et al. (2006) Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors. FEBS Lett 580: 5130-5136.
-
(2006)
FEBS Lett
, vol.580
, pp. 5130-5136
-
-
Floquet, N.1
Marechal, J.D.2
Badet-Denisot, M.A.3
Robert, C.H.4
Dauchez, M.5
-
112
-
-
58149103168
-
Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site
-
Floquet N, Durand P, Maigret B, Badet B, Badet-Denisot MA, et al. (2009) Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site. J Mol Biol 385: 653-664.
-
(2009)
J Mol Biol
, vol.385
, pp. 653-664
-
-
Floquet, N.1
Durand, P.2
Maigret, B.3
Badet, B.4
Badet-Denisot, M.A.5
-
113
-
-
67649422714
-
Fpocket: an open source platform for ligand pocket detection
-
Le GV, Schmidtke P, Tuffery P, (2009) Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics 10: 168.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 168
-
-
Le, G.V.1
Schmidtke, P.2
Tuffery, P.3
-
114
-
-
78650714726
-
Large-Scale Comparison of Four Binding Site Detection Algorithms
-
Schmidtke P, Souaille C, Estienne F, Baurin N, Kroemer RT, (2010) Large-Scale Comparison of Four Binding Site Detection Algorithms. J Chem Inf Model.
-
(2010)
J Chem Inf Model
-
-
Schmidtke, P.1
Souaille, C.2
Estienne, F.3
Baurin, N.4
Kroemer, R.T.5
-
115
-
-
48449105393
-
The RosettaDock server for local protein-protein docking
-
Lyskov S, Gray JJ, (2008) The RosettaDock server for local protein-protein docking. Nucl Acids Res 36: W233-W238.
-
(2008)
Nucl Acids Res
, vol.36
, pp. 233-238
-
-
Lyskov, S.1
Gray, J.J.2
|