-
1
-
-
0033593230
-
Bax-induced caspase activation and apoptosis via cytochrome c release from mitochondria is inhibitable by Bcl-XL
-
Finucane DM, Bossy-Wetzel E, Waterhouse NJ, Cotter TG, Green DR, (1999) Bax-induced caspase activation and apoptosis via cytochrome c release from mitochondria is inhibitable by Bcl-XL. J Biol Chem 274: 2225-2233.
-
(1999)
J Biol Chem
, vol.274
, pp. 2225-2233
-
-
Finucane, D.M.1
Bossy-Wetzel, E.2
Waterhouse, N.J.3
Cotter, T.G.4
Green, D.R.5
-
2
-
-
0030795866
-
Bcl-2 and Bcl-XL can differentially block chemotherapy-induced cell death
-
Simonian PL, Grillot DAM, Nunez G, (1997) Bcl-2 and Bcl-XL can differentially block chemotherapy-induced cell death. Blood 90: 1208-1216.
-
(1997)
Blood
, vol.90
, pp. 1208-1216
-
-
Simonian, P.L.1
Grillot, D.A.M.2
Nunez, G.3
-
3
-
-
45849112182
-
Bcl-XL inhibits membrane permeabilization by competing with Bax
-
Billen P, Kokoski CL, Lovell JF, Leber B, Andrews DW, (2008) Bcl-XL inhibits membrane permeabilization by competing with Bax. PLoS Biol 6: 1268-1280.
-
(2008)
PLoS Biol
, vol.6
, pp. 1268-1280
-
-
Billen, P.1
Kokoski, C.L.2
Lovell, J.F.3
Leber, B.4
Andrews, D.W.5
-
4
-
-
77952029788
-
Perturbation of the Bcl-2 network and an induced Noxa/Bcl-XL interaction trigger mitochondrial dysfunction after DNA damage
-
Lopez H, Zhang LQ, George NM, Liu XQ, Pang XM, et al. (2010) Perturbation of the Bcl-2 network and an induced Noxa/Bcl-XL interaction trigger mitochondrial dysfunction after DNA damage. J Biol Chem 285: 15016-15026.
-
(2010)
J Biol Chem
, vol.285
, pp. 15016-15026
-
-
Lopez, H.1
Zhang, L.Q.2
George, N.M.3
Liu, X.Q.4
Pang, X.M.5
-
5
-
-
75949105922
-
The Bcl-2 family reunion
-
Chipuk JE, Moldoveanu T, Liambi F, Parsons MJ, Green DR, (2010) The Bcl-2 family reunion. Mol Cell 37: 299-310.
-
(2010)
Mol Cell
, vol.37
, pp. 299-310
-
-
Chipuk, J.E.1
Moldoveanu, T.2
Liambi, F.3
Parsons, M.J.4
Green, D.R.5
-
6
-
-
0028950645
-
Prevention of hypoxia-induced cell death by Bcl-2 and Bcl-XL
-
Shimizu S, Eguchi Y, Kosaka H, Kamiike W, Matsuda H, et al. (1995) Prevention of hypoxia-induced cell death by Bcl-2 and Bcl-XL. Nature 374: 811-813.
-
(1995)
Nature
, vol.374
, pp. 811-813
-
-
Shimizu, S.1
Eguchi, Y.2
Kosaka, H.3
Kamiike, W.4
Matsuda, H.5
-
7
-
-
0037415861
-
Design and application of an alpha-helix mimetic scaffold based on an oligoamide-foldamer strategy: Antagonism of the bak BH3/Bcl-XL complex
-
Ernst JT, Becerril J, Park HS, Yin H, Hamilton AD, (2003) Design and application of an alpha-helix mimetic scaffold based on an oligoamide-foldamer strategy: Antagonism of the bak BH3/Bcl-XL complex. Angew Chem Int Ed Engl 42: 535.
-
(2003)
Angew Chem Int Ed Engl
, vol.42
, pp. 535
-
-
Ernst, J.T.1
Becerril, J.2
Park, H.S.3
Yin, H.4
Hamilton, A.D.5
-
8
-
-
20544437817
-
Unknotting the roles of Bcl-2 and Bcl-XL in cell death
-
Kim R, (2005) Unknotting the roles of Bcl-2 and Bcl-XL in cell death. Biochem Biophys Res Commun 333: 336-343.
-
(2005)
Biochem Biophys Res Commun
, vol.333
, pp. 336-343
-
-
Kim, R.1
-
9
-
-
0035111297
-
Insulin-like growth factor-I and over-expression of Bcl-XL prevent glucose-mediated apoptosis in Schwann cells
-
Delaney CL, Russell JW, Cheng HL, Feldman EL, (2001) Insulin-like growth factor-I and over-expression of Bcl-XL prevent glucose-mediated apoptosis in Schwann cells. J Neuropathol Exp Neurol 60: 147-160.
-
(2001)
J Neuropathol Exp Neurol
, vol.60
, pp. 147-160
-
-
Delaney, C.L.1
Russell, J.W.2
Cheng, H.L.3
Feldman, E.L.4
-
10
-
-
79956308547
-
The Bcl-2 homology domain 3 (BH3) mimetic ABT-737 reveals the dynamic regulation of Bad, a proapoptotic protein of the Bcl-2 family, by Bcl-XL
-
Ezzoukhry Z, Louandre C, Francois C, Saidak Z, Godin C, et al. (2011) The Bcl-2 homology domain 3 (BH3) mimetic ABT-737 reveals the dynamic regulation of Bad, a proapoptotic protein of the Bcl-2 family, by Bcl-XL. Mol Pharmacol 79: 997-1004.
-
(2011)
Mol Pharmacol
, vol.79
, pp. 997-1004
-
-
Ezzoukhry, Z.1
Louandre, C.2
Francois, C.3
Saidak, Z.4
Godin, C.5
-
11
-
-
0034071150
-
Induction of apoptosis in lung-cancer cells following Bcl-XL anti-sense treatment
-
Leech SH, Olie RA, Gautschi O, Simoes-Wust AP, Tschopp S, et al. (2000) Induction of apoptosis in lung-cancer cells following Bcl-XL anti-sense treatment. Int J Cancer 86: 570-576.
-
(2000)
Int J Cancer
, vol.86
, pp. 570-576
-
-
Leech, S.H.1
Olie, R.A.2
Gautschi, O.3
Simoes-Wust, A.P.4
Tschopp, S.5
-
12
-
-
20144387336
-
Bcl-XL small interfering RNA suppresses the proliferation of 5-fluorouracil-resistant human colon cancer cells
-
Zhu HB, Guo W, Zhang LD, Davis JJ, Teraishi F, et al. (2005) Bcl-XL small interfering RNA suppresses the proliferation of 5-fluorouracil-resistant human colon cancer cells. Mol Cancer Ther 4: 451-456.
-
(2005)
Mol Cancer Ther
, vol.4
, pp. 451-456
-
-
Zhu, H.B.1
Guo, W.2
Zhang, L.D.3
Davis, J.J.4
Teraishi, F.5
-
13
-
-
0032471711
-
Moderate activation of the apoptosis inhibitor Bcl-XL worsens the prognosis in pancreatic cancer
-
Friess H, Lu Z, Andren-Sandberg A, Berberat P, Zimmermann A, et al. (1998) Moderate activation of the apoptosis inhibitor Bcl-XL worsens the prognosis in pancreatic cancer. Ann Surgery 228: 780-787.
-
(1998)
Ann Surgery
, vol.228
, pp. 780-787
-
-
Friess, H.1
Lu, Z.2
Andren-Sandberg, A.3
Berberat, P.4
Zimmermann, A.5
-
14
-
-
0033902003
-
Bcl-XL antisense treatment induces apoptosis in breast carcinoma cells
-
Simoes-Wust AP, Olie RA, Gautschi O, Leech SH, Haner R, et al. (2000) Bcl-XL antisense treatment induces apoptosis in breast carcinoma cells. Int J Cancer 87: 562-590.
-
(2000)
Int J Cancer
, vol.87
, pp. 562-590
-
-
Simoes-Wust, A.P.1
Olie, R.A.2
Gautschi, O.3
Leech, S.H.4
Haner, R.5
-
15
-
-
0034326272
-
Bcl-XL in prostate cancer cells: Effects of overexpression and down-regulation on chemosensitivity
-
Lebedeva I, Rando R, Ojwang J, Cossum P, Stein CA, (2000) Bcl-XL in prostate cancer cells: Effects of overexpression and down-regulation on chemosensitivity. Cancer Res 60: 6052-6060.
-
(2000)
Cancer Res
, vol.60
, pp. 6052-6060
-
-
Lebedeva, I.1
Rando, R.2
Ojwang, J.3
Cossum, P.4
Stein, C.A.5
-
16
-
-
79952112980
-
Drugs targeting Bcl-2 family members as an emerging strategy in cancer
-
Art. no.e28
-
Leber B, Geng F, Kale J, Andrews DW, (2010) Drugs targeting Bcl-2 family members as an emerging strategy in cancer. Expert Rev Mol Med 12: Art. no.e28 http://journals.cambridge.org/abstract_S1462399410001572.
-
(2010)
Expert Rev Mol Med
, vol.12
-
-
Leber, B.1
Geng, F.2
Kale, J.3
Andrews, D.W.4
-
17
-
-
84860508708
-
Bcl-2 inhibitors: Emerging drugs in cancer therapy
-
Bodur C, Basaga H, (2012) Bcl-2 inhibitors: Emerging drugs in cancer therapy. Curr Med Chem 19: 1804-1820.
-
(2012)
Curr Med Chem
, vol.19
, pp. 1804-1820
-
-
Bodur, C.1
Basaga, H.2
-
19
-
-
0030614915
-
Structure of Bcl-xL-Bak peptide complex: Recognition between regulators of apoptosis
-
Sattler M, Liang H, Nettesheim DG, Meadows RP, Harlan JE, et al. (1997) Structure of Bcl-xL-Bak peptide complex: Recognition between regulators of apoptosis. Science 275: 983-986.
-
(1997)
Science
, vol.275
, pp. 983-986
-
-
Sattler, M.1
Liang, H.2
Nettesheim, D.G.3
Meadows, R.P.4
Harlan, J.E.5
-
20
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliand G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliand, G.4
Bhat, T.N.5
-
21
-
-
0035853130
-
Solution structure of the antiapoptotic protein bcl-2
-
Petros AM, Medek A, Nettesheim DG, Kim DH, Yoon HS, et al. (2001) Solution structure of the antiapoptotic protein bcl-2. Proc Natl Acad Sci USA 98: 3012-3017.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 3012-3017
-
-
Petros, A.M.1
Medek, A.2
Nettesheim, D.G.3
Kim, D.H.4
Yoon, H.S.5
-
22
-
-
19944432123
-
Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function
-
Chen L, Willis SN, Wei A, Smith BJ, Fletcher JI, et al. (2005) Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function. Mol Cell 17: 393-403.
-
(2005)
Mol Cell
, vol.17
, pp. 393-403
-
-
Chen, L.1
Willis, S.N.2
Wei, A.3
Smith, B.J.4
Fletcher, J.I.5
-
23
-
-
80052175637
-
Structural basis of Bcl-x(L) recognition by a BH3-mimetic alpha/beta-peptide generated by sequence-based design
-
Lee EF, Smith BJ, Horne WS, Mayer KN, Evangelista M, et al. (2011) Structural basis of Bcl-x(L) recognition by a BH3-mimetic alpha/beta-peptide generated by sequence-based design. ChemBiochem 12: 2025-2032.
-
(2011)
ChemBiochem
, vol.12
, pp. 2025-2032
-
-
Lee, E.F.1
Smith, B.J.2
Horne, W.S.3
Mayer, K.N.4
Evangelista, M.5
-
24
-
-
79959713674
-
Rational design of new class of BH3-mimetics as inhibitors of the Bcl-XL protein
-
Pinto M, del Mar Orzaez M, Delgado-Soler L, Perez JJ, Rubio-Martinez J, (2011) Rational design of new class of BH3-mimetics as inhibitors of the Bcl-XL protein. J Chem Inf Model 51: 1249-1258.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 1249-1258
-
-
Pinto, M.1
del Mar Orzaez, M.2
Delgado-Soler, L.3
Perez, J.J.4
Rubio-Martinez, J.5
-
25
-
-
79953222918
-
The BH3 alpha-helical mimic BH3-M6 disrupts Bcl-XL, Bcl-2, and MCL-1 protein-protein interactions with Bax, Bad, or Bim and induces apoptosis in a Bax- and Bim-dependent manner
-
Kazi A, Sun J, Doi K, Sung S-S, Takahashi Y, et al. (2011) The BH3 alpha-helical mimic BH3-M6 disrupts Bcl-XL, Bcl-2, and MCL-1 protein-protein interactions with Bax, Bad, or Bim and induces apoptosis in a Bax- and Bim-dependent manner. J Biol Chem 286: 9382-9392.
-
(2011)
J Biol Chem
, vol.286
, pp. 9382-9392
-
-
Kazi, A.1
Sun, J.2
Doi, K.3
Sung, S.-S.4
Takahashi, Y.5
-
26
-
-
84858957935
-
Relaxation of the rigid backbone of an oligoamide-foldamer-based alpha-helix mimetic: identification of potent Bcl-XL inhibitors
-
Yap JL, Cao XB, Vanommeslaeghe K, Jung KY, Peddaboina C, et al. (2012) Relaxation of the rigid backbone of an oligoamide-foldamer-based alpha-helix mimetic: identification of potent Bcl-XL inhibitors. Org Biomol Chem 10: 2928-2933.
-
(2012)
Org Biomol Chem
, vol.10
, pp. 2928-2933
-
-
Yap, J.L.1
Cao, X.B.2
Vanommeslaeghe, K.3
Jung, K.Y.4
Peddaboina, C.5
-
27
-
-
77957844567
-
3D-QSAR pharmacophore modeling and in silico screening of new Bcl-xl inhibitors
-
Almerico AM, Tutone M, Lauria A, (2010) 3D-QSAR pharmacophore modeling and in silico screening of new Bcl-xl inhibitors. Eur J Med Chem 45: 4774-4782.
-
(2010)
Eur J Med Chem
, vol.45
, pp. 4774-4782
-
-
Almerico, A.M.1
Tutone, M.2
Lauria, A.3
-
28
-
-
77952788585
-
Targeting the BH3 domain mediated protein-protein interaction of Bcl-XL through virtual screening
-
Mukherjee P, Desai P, Zhou Y-D, Avery M, (2010) Targeting the BH3 domain mediated protein-protein interaction of Bcl-XL through virtual screening. J Chem Inf Model 50: 906-923.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 906-923
-
-
Mukherjee, P.1
Desai, P.2
Zhou, Y.-D.3
Avery, M.4
-
29
-
-
77949837779
-
Fragment-based deconstruction of Bcl-XL inhibitors
-
Barelier S, Pons J, Marcillat O, Lancelin J-M, Krimm I, (2010) Fragment-based deconstruction of Bcl-XL inhibitors. J Med Chem 53: 2577-2588.
-
(2010)
J Med Chem
, vol.53
, pp. 2577-2588
-
-
Barelier, S.1
Pons, J.2
Marcillat, O.3
Lancelin, J.-M.4
Krimm, I.5
-
30
-
-
52249106626
-
Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: Comparative molecular dynamics simulations
-
Lama D, Sankararamakrishnan R, (2008) Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: Comparative molecular dynamics simulations. Proteins 73: 492-514.
-
(2008)
Proteins
, vol.73
, pp. 492-514
-
-
Lama, D.1
Sankararamakrishnan, R.2
-
31
-
-
17744396094
-
Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies
-
Petros AM, Nettesheim DG, Wang Y, Olejniczak ET, Meadows RP, et al. (2000) Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies. Protein Sci 9: 2528-2534.
-
(2000)
Protein Sci
, vol.9
, pp. 2528-2534
-
-
Petros, A.M.1
Nettesheim, D.G.2
Wang, Y.3
Olejniczak, E.T.4
Meadows, R.P.5
-
32
-
-
80051693048
-
Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: Relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-XL
-
Lama D, Sankararamakrishnan R, (2011) Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: Relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-XL. J Comput Aided Mol Des 25: 413-426.
-
(2011)
J Comput Aided Mol Des
, vol.25
, pp. 413-426
-
-
Lama, D.1
Sankararamakrishnan, R.2
-
33
-
-
84871201320
-
Relationship between helix stability and binding affinities: Molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent
-
Modi V, Lama D, Sankararamakrishnan R, (2013) Relationship between helix stability and binding affinities: Molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent. J Biomol Struct Dyn 31: 65-77.
-
(2013)
J Biomol Struct Dyn
, vol.31
, pp. 65-77
-
-
Modi, V.1
Lama, D.2
Sankararamakrishnan, R.3
-
34
-
-
33646354381
-
Mitochondria primed by death signals determine cellular addiction to antiapoptotic BCL-2 family members
-
Certo M, Moore VD, Nishino M, Wei G, Korsmeyer S, et al. (2006) Mitochondria primed by death signals determine cellular addiction to antiapoptotic BCL-2 family members. Cancer Cell 9: 351-365.
-
(2006)
Cancer Cell
, vol.9
, pp. 351-365
-
-
Certo, M.1
Moore, V.D.2
Nishino, M.3
Wei, G.4
Korsmeyer, S.5
-
35
-
-
43049105074
-
To trigger apoptosis, Bak exposes its BH3 domain and homodimerizes via BH3:groove interactions
-
Dewson G, Kratina T, Sim HW, Puthalakath H, Adams JM, et al. (2008) To trigger apoptosis, Bak exposes its BH3 domain and homodimerizes via BH3:groove interactions. Mol Cell 30: 369-380.
-
(2008)
Mol Cell
, vol.30
, pp. 369-380
-
-
Dewson, G.1
Kratina, T.2
Sim, H.W.3
Puthalakath, H.4
Adams, J.M.5
-
36
-
-
84858158794
-
Bax dimerizes via symmetric BH3:groove interface during apoptosis
-
Dewson G, Ma S, Frederick P, Hockings C, Tan I, et al. (2012) Bax dimerizes via symmetric BH3:groove interface during apoptosis. Cell Death Differ 19: 661-670.
-
(2012)
Cell Death Differ
, vol.19
, pp. 661-670
-
-
Dewson, G.1
Ma, S.2
Frederick, P.3
Hockings, C.4
Tan, I.5
-
37
-
-
0042220409
-
The structure of a Bcl-xL/Bim fragment complex: Implications for Bim function
-
Liu X, Dai S, Zhu Y, Marrack P, Kappler JW, (2003) The structure of a Bcl-xL/Bim fragment complex: Implications for Bim function. Immunity 19: 341-352.
-
(2003)
Immunity
, vol.19
, pp. 341-352
-
-
Liu, X.1
Dai, S.2
Zhu, Y.3
Marrack, P.4
Kappler, J.W.5
-
38
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
Consortium TU, (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-D75.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Consortium, T.U.1
-
39
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: Fast, flexible, and free. J Comput Chem 26: 1701-1718.
-
(2005)
J Comput Chem
, vol.26
, pp. 1701-1718
-
-
van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
-
40
-
-
0035789518
-
Gromacs 3.0: A package for molecular simulation
-
Lindahl E, Hess B, van der Spoel D, (2001) Gromacs 3.0: A package for molecular simulation. J Mol Model 7: 306-317.
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
41
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
In. Pullman B, Ed. The Netherlands Reidel
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. (1981) Interaction models for water in relation to protein hydration. In. Pullman B, Ed.Intermolecular Forces Dordrecht, The Netherlands Reidel pp 331-342.
-
(1981)
Intermolecular Forces Dordrecht
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Hermans, J.4
-
42
-
-
0001751804
-
Parametrization of aliphatic CHn united atoms of GROMOS96 force field
-
Daura X, Mark AE, van Gunsteren WF, (1998) Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J Comput Chem 19: 535-547.
-
(1998)
J Comput Chem
, vol.19
, pp. 535-547
-
-
Daura, X.1
Mark, A.E.2
van Gunsteren, W.F.3
-
43
-
-
0001886497
-
Biomolecular simulation: The GROMOS96 manual and user guide
-
van Gunsteren WF, Billeter SR, Eising AA, Hunenberger PH, Kruger P, et al. (1996) Biomolecular simulation: The GROMOS96 manual and user guide. Vdf Hochschulverlag AG an der ETH Zurich, Switzerland pp. 1-1042.
-
(1996)
Vdf Hochschulverlag AG an Der ETH Zurich, Switzerland
, pp. 1-1042
-
-
van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hunenberger, P.H.4
Kruger, P.5
-
44
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto S, Kollman PA, (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13: 952-962.
-
(1992)
J Comput Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
45
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM, (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18: 1463-1472.
-
(1997)
J Comput Chem
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
46
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren 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
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
47
-
-
0034062925
-
Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures
-
Eswar N, Ramakrishnan C, (2000) Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Eng 13: 227-238.
-
(2000)
Protein Eng
, vol.13
, pp. 227-238
-
-
Eswar, N.1
Ramakrishnan, C.2
-
48
-
-
0041784950
-
All atom empirical potential for molecular modeling and dynamics studies of proteins
-
Mackerell AD Jr, Bashford D, Bellot M, Dunbrack RL, Evanseck JD, et al. (1998) All atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell Jr., A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
-
49
-
-
71049128694
-
Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind their ligands
-
Lee EF, Czabotar PE, Yang H, Sleebs BE, Lessene G, et al. (2009) Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind their ligands. J Biol Chem 284: 30508-30517.
-
(2009)
J Biol Chem
, vol.284
, pp. 30508-30517
-
-
Lee, E.F.1
Czabotar, P.E.2
Yang, H.3
Sleebs, B.E.4
Lessene, G.5
-
50
-
-
42949110343
-
Structural plasticity underpins promiscuous binding of the prosurvival protein A1
-
Smits C, Czabotar PE, Hinds MG, Day CL, (2008) Structural plasticity underpins promiscuous binding of the prosurvival protein A1. Structure 16: 818-829.
-
(2008)
Structure
, vol.16
, pp. 818-829
-
-
Smits, C.1
Czabotar, P.E.2
Hinds, M.G.3
Day, C.L.4
-
51
-
-
0029067489
-
Specificity of ligand-binding in a buried nonpolar cavity of T4 lysozyme - linkage dynamics and structural plasticity
-
Morton A, Matthews BW, (1995) Specificity of ligand-binding in a buried nonpolar cavity of T4 lysozyme- linkage dynamics and structural plasticity. Biochemistry 34: 8576-8588.
-
(1995)
Biochemistry
, vol.34
, pp. 8576-8588
-
-
Morton, A.1
Matthews, B.W.2
-
52
-
-
34547653666
-
Structural plasticity in the oestrogen receptor ligand-binding domain
-
Nettles KW, Bruning JB, Gil G, O'Neill EE, Nowak J, et al. (2007) Structural plasticity in the oestrogen receptor ligand-binding domain. EMBO Rep 8: 563-568.
-
(2007)
EMBO Rep
, vol.8
, pp. 563-568
-
-
Nettles, K.W.1
Bruning, J.B.2
Gil, G.3
O'Neill, E.E.4
Nowak, J.5
-
53
-
-
79958772218
-
Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity
-
Silva D-A, Dominguez-Ramirez L, Rojo-Dominguez A, Sosa-Peinado A, (2011) Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity. Proteins 79: 2097-2108.
-
(2011)
Proteins
, vol.79
, pp. 2097-2108
-
-
Silva, D.-A.1
Dominguez-Ramirez, L.2
Rojo-Dominguez, A.3
Sosa-Peinado, A.4
-
54
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438: 117-121.
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
-
55
-
-
77949507320
-
Identification of core structural residues in sequentially diverse and structurally homologous Bcl-2 family of proteins
-
Lama D, Sankararamakrishnan R, (2010) Identification of core structural residues in sequentially diverse and structurally homologous Bcl-2 family of proteins. Biochemistry 49: 2574-2584.
-
(2010)
Biochemistry
, vol.49
, pp. 2574-2584
-
-
Lama, D.1
Sankararamakrishnan, R.2
-
56
-
-
0030862687
-
The BH3 domain of Bax is sufficient for interaction of Bax with itself and with other family members and it is required for induction of apoptosis
-
Simonen M, Keller H, Heim J, (1997) The BH3 domain of Bax is sufficient for interaction of Bax with itself and with other family members and it is required for induction of apoptosis. Eur J Biochem 249: 85-91.
-
(1997)
Eur J Biochem
, vol.249
, pp. 85-91
-
-
Simonen, M.1
Keller, H.2
Heim, J.3
-
57
-
-
0030995943
-
A common binding site mediates heterodimerization and homodimerization of Bcl-2 family members
-
Diaz JL, Oltersdorf T, Horne WS, McConnell M, Wilson G, et al. (1997) A common binding site mediates heterodimerization and homodimerization of Bcl-2 family members. J Biol Chem 272: 11350-11355.
-
(1997)
J Biol Chem
, vol.272
, pp. 11350-11355
-
-
Diaz, J.L.1
Oltersdorf, T.2
Horne, W.S.3
McConnell, M.4
Wilson, G.5
-
58
-
-
0037199456
-
Peptides derived from BH3 domains of Bcl-2 members: A comparative analysis of inhibition of Bcl-2, Bcl-XL and Bax oligomerization, induction of cytochrome c release, and activation of cell death
-
Shangary S, Johnson DE, (2002) Peptides derived from BH3 domains of Bcl-2 members: A comparative analysis of inhibition of Bcl-2, Bcl-XL and Bax oligomerization, induction of cytochrome c release, and activation of cell death. Biochemistry 41: 9485-9495.
-
(2002)
Biochemistry
, vol.41
, pp. 9485-9495
-
-
Shangary, S.1
Johnson, D.E.2
-
59
-
-
0344608883
-
The structure of Bcl-w reveals a role for the C-terminal residues in modulating biological activity
-
Hinds MG, Lackmann M, Skea GL, Harrison PJ, Huang DCS, et al. (2003) The structure of Bcl-w reveals a role for the C-terminal residues in modulating biological activity. EMBO J 22: 1497-1507.
-
(2003)
EMBO J
, vol.22
, pp. 1497-1507
-
-
Hinds, M.G.1
Lackmann, M.2
Skea, G.L.3
Harrison, P.J.4
Huang, D.C.S.5
-
60
-
-
14244265108
-
Solution structure of prosurvival Mcl-1 and characterization of its binding by proapoptotic BH3-only ligands
-
Day CL, Chen L, Richardson SJ, Harrison PJ, Huang DCS, et al. (2005) Solution structure of prosurvival Mcl-1 and characterization of its binding by proapoptotic BH3-only ligands. J Biol Chem 280: 4738-4744.
-
(2005)
J Biol Chem
, vol.280
, pp. 4738-4744
-
-
Day, C.L.1
Chen, L.2
Richardson, S.J.3
Harrison, P.J.4
Huang, D.C.S.5
-
61
-
-
0346457100
-
Bcl-XL mutations supress cellular sensitivity to antimycin A
-
Manion MK, O'Neil JW, Giedt CD, Kim KM, Zhang KYZ, et al. (2004) Bcl-XL mutations supress cellular sensitivity to antimycin A. J Biol Chem 279: 2159-2165.
-
(2004)
J Biol Chem
, vol.279
, pp. 2159-2165
-
-
Manion, M.K.1
O'Neil, J.W.2
Giedt, C.D.3
Kim, K.M.4
Zhang, K.Y.Z.5
-
62
-
-
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
-
63
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103: 8577-8593.
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
-
64
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems - The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Chetham TE, Miller JL, Fox T, Darden T, Kollman PA, (1995) Molecular dynamics simulations on solvated biomolecular systems- The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 117: 4193-4194.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 4193-4194
-
-
Chetham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.4
Kollman, P.A.5
-
65
-
-
73949107784
-
Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supecomputer
-
Schulz R, Lindner B, Petridis L, Smith JC, (2009) Scaling of multimillion-atom biological molecular dynamics simulation on a petascale supecomputer. J Chem Theory Comput 5: 2798-2808.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2798-2808
-
-
Schulz, R.1
Lindner, B.2
Petridis, L.3
Smith, J.C.4
-
66
-
-
73549108553
-
Effects of long-range electrostatics on time-dependent stokes shift calculations
-
Furse KE, Corcelli SA, (2009) Effects of long-range electrostatics on time-dependent stokes shift calculations. J Chem Theory Comput 5: 1959-1967.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 1959-1967
-
-
Furse, K.E.1
Corcelli, S.A.2
-
67
-
-
33947732290
-
Effect of different treatments of long-range interactions and sampling conditions in molecular dynamics simulations of rhodopsin embedded in dipalmitoylphosphatidylcholine bilayer
-
Cordomi A, Edholm O, Perez JJ, (2007) Effect of different treatments of long-range interactions and sampling conditions in molecular dynamics simulations of rhodopsin embedded in dipalmitoylphosphatidylcholine bilayer. J Comput Chem 28: 1017-1030.
-
(2007)
J Comput Chem
, vol.28
, pp. 1017-1030
-
-
Cordomi, A.1
Edholm, O.2
Perez, J.J.3
-
68
-
-
33645310406
-
Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides
-
Monticelli L, Simoes C, Belvisi L, Colombo G, (2006) Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides. J Phys Condens Matter 18: S329-S345.
-
(2006)
J Phys Condens Matter
, vol.18
-
-
Monticelli, L.1
Simoes, C.2
Belvisi, L.3
Colombo, G.4
-
69
-
-
33846231365
-
Influence of long-range electrostatic treatments on the folding of the N-terminal H4 histone tail peptide
-
Lins RD, Rothlisberger U, (2006) Influence of long-range electrostatic treatments on the folding of the N-terminal H4 histone tail peptide. J Chem Theory Comput 2: 246-250.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 246-250
-
-
Lins, R.D.1
Rothlisberger, U.2
-
70
-
-
25144520249
-
On the Ewald artifacts in computer simulations. The test case of octaalanine peptide with charged termini
-
Villarreal MA, Montich GG, (2005) On the Ewald artifacts in computer simulations. The test case of octaalanine peptide with charged termini. J Biomol Struct Dyn 23: 135-142.
-
(2005)
J Biomol Struct Dyn
, vol.23
, pp. 135-142
-
-
Villarreal, M.A.1
Montich, G.G.2
-
71
-
-
4143094922
-
The influence of simulation conditions in molecular dynamics investigations of model beta-sheet peptides
-
Monticelli L, Colombo G, (2004) The influence of simulation conditions in molecular dynamics investigations of model beta-sheet peptides. Ther Chem Acc 112: 145-157.
-
(2004)
Ther Chem Acc
, vol.112
, pp. 145-157
-
-
Monticelli, L.1
Colombo, G.2
-
72
-
-
0343005873
-
Molecular dynamics simulations of a polyalanine octapeptide under ewald boundary conditions: influence of artificial periodicity on peptide conformation
-
Weber W, Hunenberger PH, McCammon JA, (2000) Molecular dynamics simulations of a polyalanine octapeptide under ewald boundary conditions: influence of artificial periodicity on peptide conformation. J Phys Chem B 104: 3668-3675.
-
(2000)
J Phys Chem B
, vol.104
, pp. 3668-3675
-
-
Weber, W.1
Hunenberger, P.H.2
McCammon, J.A.3
-
73
-
-
0037627173
-
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study
-
Hunenberger PH, McCammon JA, (1999) Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem 78: 69-88.
-
(1999)
Biophys Chem
, vol.78
, pp. 69-88
-
-
Hunenberger, P.H.1
McCammon, J.A.2
-
74
-
-
0036841855
-
Analysis and evaluation of channel models: Simulations of alamethicin
-
Tieleman DP, Hess B, Sansom MSP, (2002) Analysis and evaluation of channel models: Simulations of alamethicin. Biophys J 83: 2392-2407.
-
(2002)
Biophys J
, vol.83
, pp. 2392-2407
-
-
Tieleman, D.P.1
Hess, B.2
Sansom, M.S.P.3
-
75
-
-
76149102555
-
Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers
-
Prakash P, Sankararamakrishnan R, (2010) Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers. J Comput Chem 31: 266-277.
-
(2010)
J Comput Chem
, vol.31
, pp. 266-277
-
-
Prakash, P.1
Sankararamakrishnan, R.2
-
76
-
-
84860605119
-
Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations
-
Venken T, Daelemans D, De Maeyer M, Voet A, (2012) Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations. Proteins 80: 1633-1646.
-
(2012)
Proteins
, vol.80
, pp. 1633-1646
-
-
Venken, T.1
Daelemans, D.2
De Maeyer, M.3
Voet, A.4
-
77
-
-
84862166136
-
Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers
-
Issack BB, Berjanskii M, Wishart DS, Stepanova M, (2012) Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers. Proteins 80: 1847-1865.
-
(2012)
Proteins
, vol.80
, pp. 1847-1865
-
-
Issack, B.B.1
Berjanskii, M.2
Wishart, D.S.3
Stepanova, M.4
-
78
-
-
84855973765
-
Structural coupling between the Rho-insert domain of Cdc42 and geranylgeranyl binding site of RhoGDI
-
Abramovitz A, Gutman M, Nachliel E, (2012) Structural coupling between the Rho-insert domain of Cdc42 and geranylgeranyl binding site of RhoGDI. Biochemistry 51: 715-723.
-
(2012)
Biochemistry
, vol.51
, pp. 715-723
-
-
Abramovitz, A.1
Gutman, M.2
Nachliel, E.3
-
79
-
-
79955739413
-
Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle
-
Karthik S, Senapati S, (2011) Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle. Proteins 79: 1830-1840.
-
(2011)
Proteins
, vol.79
, pp. 1830-1840
-
-
Karthik, S.1
Senapati, S.2
-
80
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang JM, Cieplak P, Kollman PA, (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21: 1049-1074.
-
(2000)
J Comput Chem
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
81
-
-
79954613990
-
Hydrophobic binding hot spots of Bcl-xL protein-protein interfaces by cosolvent molecular dynamics simulation
-
Yang C-Y, Wang S, (2011) Hydrophobic binding hot spots of Bcl-xL protein-protein interfaces by cosolvent molecular dynamics simulation. ACS Med Chem Lett 2: 280-284.
-
(2011)
ACS Med Chem Lett
, vol.2
, pp. 280-284
-
-
Yang, C.-Y.1
Wang, S.2
-
82
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4: 435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
83
-
-
78149463926
-
Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact
-
Florova P, Sklenovsky P, Banas P, Otyepka M, (2010) Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact. J Chem Theory Comput 6: 3569-3579.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 3569-3579
-
-
Florova, P.1
Sklenovsky, P.2
Banas, P.3
Otyepka, M.4
-
85
-
-
43749107283
-
Comparative protein structure modeling using Modeller
-
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2006) Comparative protein structure modeling using Modeller. Curr Protocols Bioinf Supp. 15: 5.6.1-5.6.30.
-
(2006)
Curr Protocols Bioinf
, Issue.SUPPL. 15
, pp. 1-30
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
|