-
1
-
-
80055056709
-
A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death
-
Atkinson J, Kapralov AA, Yanamala N, Tyurina YY, Amoscato AA, Pearce L, Peterson J, Huang Z, Jiang J, and Samhan-Arias AK et al. (2011) A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death. Nat Commun 2:497.
-
(2011)
Nat Commun
, vol.2
, pp. 497
-
-
Atkinson, J.1
Kapralov, A.A.2
Yanamala, N.3
Tyurina, Y.Y.4
Amoscato, A.A.5
Pearce, L.6
Peterson, J.7
Huang, Z.8
Jiang, J.9
Samhan-Arias, A.K.10
-
2
-
-
77950571108
-
New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays
-
Baell JB and Holloway GA (2010) New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 53:2719-2740.
-
(2010)
J Med Chem
, vol.53
, pp. 2719-2740
-
-
Baell, J.B.1
Holloway, G.A.2
-
3
-
-
84907486031
-
Evol and ProDy for bridging protein sequence evolution and structural dynamics
-
Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, and Bahar I (2014) Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics 30:2681-2683.
-
(2014)
Bioinformatics
, vol.30
, pp. 2681-2683
-
-
Bakan, A.1
Dutta, A.2
Mao, W.3
Liu, Y.4
Chennubhotla, C.5
Lezon, T.R.6
Bahar, I.7
-
4
-
-
84863661333
-
Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules
-
Bakan A, Nevins N, Lakdawala AS, and Bahar I (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules. J Chem Theory Comput 8:2435-2447.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2435-2447
-
-
Bakan, A.1
Nevins, N.2
Lakdawala, A.S.3
Bahar, I.4
-
5
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, and Bourne PE (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
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
6
-
-
0025007598
-
High-resolution three-dimensional structure of horse heart cytochrome c
-
Bushnell GW, Louie GV, and Brayer GD (1990) High-resolution three-dimensional structure of horse heart cytochrome c. J Mol Biol 214:585-595.
-
(1990)
J Mol Biol
, vol.214
, pp. 585-595
-
-
Bushnell, G.W.1
Louie, G.V.2
Brayer, G.D.3
-
7
-
-
84856011942
-
Conformational properties of cardiolipin-bound cytochrome c
-
Hanske J, Toffey JR, Morenz AM, Bonilla AJ, Schiavoni KH, and Pletneva EV (2012) Conformational properties of cardiolipin-bound cytochrome c. Proc Natl Acad Sci USA 109:125-130.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 125-130
-
-
Hanske, J.1
Toffey, J.R.2
Morenz, A.M.3
Bonilla, A.J.4
Schiavoni, K.H.5
Pletneva, E.V.6
-
8
-
-
77951986384
-
Conformer generation with OMEGA: Algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database
-
Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, and Stahl MT (2010) Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model 50:572-584.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 572-584
-
-
Hawkins, P.C.D.1
Skillman, A.G.2
Warren, G.L.3
Ellingson, B.A.4
Stahl, M.T.5
-
10
-
-
13844312649
-
ZINC - A free database of commercially available compounds for virtual screening
-
Irwin JJ and Shoichet BK (2005) ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 45:177-182.
-
(2005)
J Chem Inf Model
, vol.45
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
11
-
-
84898831522
-
Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: Mitochondria-targeted imidazole-substituted fatty acids
-
Jiang J, Bakan A, Kapralov AA, Silva KI, Huang Z, Amoscato AA, Peterson J, Garapati VK, Saxena S, and Bayir H et al. (2014) Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids. Free Radic Biol Med 71:221-230.
-
(2014)
Free Radic Biol Med
, vol.71
, pp. 221-230
-
-
Jiang, J.1
Bakan, A.2
Kapralov, A.A.3
Silva, K.I.4
Huang, Z.5
Amoscato, A.A.6
Peterson, J.7
Garapati, V.K.8
Saxena, S.9
Bayir, H.10
-
12
-
-
58149350432
-
Mitochondria-targeted disruptors and inhibitors of cytochrome c/cardiolipin peroxidase complexes: A new strategy in anti-apoptotic drug discovery
-
Kagan VE, Bayir A, Bayir H, Stoyanovsky D, Borisenko GG, Tyurina YY, Wipf P, Atkinson J, Greenberger JS, and Chapkin RS et al. (2009a) Mitochondria-targeted disruptors and inhibitors of cytochrome c/cardiolipin peroxidase complexes: a new strategy in anti-apoptotic drug discovery. Mol Nutr Food Res 53:104-114.
-
(2009)
Mol Nutr Food Res
, vol.53
, pp. 104-114
-
-
Kagan, V.E.1
Bayir, A.2
Bayir, H.3
Stoyanovsky, D.4
Borisenko, G.G.5
Tyurina, Y.Y.6
Wipf, P.7
Atkinson, J.8
Greenberger, J.S.9
Chapkin, R.S.10
-
13
-
-
67349260782
-
Cytochrome c/cardiolipin relations in mitochondria: A kiss of death
-
Kagan VE, Bayir HA, Belikova NA, Kapralov O, Tyurina YY, Tyurin VA, Jiang J, Stoyanovsky DA, Wipf P, and Kochanek PM et al. (2009b) Cytochrome c/cardiolipin relations in mitochondria: a kiss of death. Free Radic Biol Med 46: 1439-1453.
-
(2009)
Free Radic Biol Med
, vol.46
, pp. 1439-1453
-
-
Kagan, V.E.1
Bayir, H.A.2
Belikova, N.A.3
Kapralov, O.4
Tyurina, Y.Y.5
Tyurin, V.A.6
Jiang, J.7
Stoyanovsky, D.A.8
Wipf, P.9
Kochanek, P.M.10
-
14
-
-
27744433524
-
Cytochrome c acts as a cardiolipin oxygenase required for release of proapoptotic factors
-
Kagan VE, Tyurin VA, Jiang J, Tyurina YY, Ritov VB, Amoscato AA, Osipov AN, Belikova NA, Kapralov AA, and Kini V et al. (2005) Cytochrome c acts as a cardiolipin oxygenase required for release of proapoptotic factors. Nat Chem Biol 1:223-232.
-
(2005)
Nat Chem Biol
, vol.1
, pp. 223-232
-
-
Kagan, V.E.1
Tyurin, V.A.2
Jiang, J.3
Tyurina, Y.Y.4
Ritov, V.B.5
Amoscato, A.A.6
Osipov, A.N.7
Belikova, N.A.8
Kapralov, A.A.9
Kini, V.10
-
15
-
-
78651287426
-
DrugBank 3.0: A comprehensive resource for 'omics' research on drugs
-
Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, and Neveu V et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res 39:D1035-D1041.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D1035-D1041
-
-
Knox, C.1
Law, V.2
Jewison, T.3
Liu, P.4
Ly, S.5
Frolkis, A.6
Pon, A.7
Banco, K.8
Mak, C.9
Neveu, V.10
-
16
-
-
0000224283
-
CHARMM: The energy function and its parameterization
-
John Wiley & Sons, Chichester, UK
-
MacKerell AD, Brooks B, Brooks C, Nilsson L, Roux B, Won Y, and Karplus M (2002) CHARMM: the energy function and Its parameterization. Encyclopedia of Computational Chemistry John Wiley & Sons, Chichester, UK.
-
(2002)
Encyclopedia of Computational Chemistry
-
-
MacKerell, A.D.1
Brooks, B.2
Brooks, C.3
Nilsson, L.4
Roux, B.5
Won, Y.6
Karplus, M.7
-
17
-
-
16344382372
-
Protein folding: The stepwise assembly of foldon units
-
Maity H, Maity M, Krishna MMG, Mayne L, and Englander SW (2005) Protein folding: the stepwise assembly of foldon units. Proc Natl Acad Sci USA 102: 4741-4746.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4741-4746
-
-
Maity, H.1
Maity, M.2
Krishna, M.M.G.3
Mayne, L.4
Englander, S.W.5
-
18
-
-
8344276781
-
NAMD: A parallel, object-oriented molecular dynamics program
-
Nelson MT, Humphrey W, Gursoy A, Dalke A, Kale LV, Skeel RD, and Schulten K (1996) NAMD: a parallel, object-oriented molecular dynamics program. Int J High Perform Comput Appl 10:251-268.
-
(1996)
Int J High Perform Comput Appl
, vol.10
, pp. 251-268
-
-
Nelson, M.T.1
Humphrey, W.2
Gursoy, A.3
Dalke, A.4
Kale, L.V.5
Skeel, R.D.6
Schulten, K.7
-
19
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, and Ferrin TE (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
20
-
-
14944348527
-
A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
-
Rush TS, 3rd, Grant JA, Mosyak L, and Nicholls A (2005) A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem 48:1489-1495.
-
(2005)
J Med Chem
, vol.48
, pp. 1489-1495
-
-
Rush, T.S.1
Grant, J.A.2
Mosyak, L.3
Nicholls, A.4
-
21
-
-
77953248538
-
Extended cardiolipin anchorage to cytochrome c: A model for protein-mitochondrial membrane binding
-
Sinibaldi F, Howes BD, Piro MC, Polticelli F, Bombelli C, Ferri T, Coletta M, Smulevich G, and Santucci R (2010) Extended cardiolipin anchorage to cytochrome c: a model for protein-mitochondrial membrane binding. J Biol Inorg Chem 15: 689-700.
-
(2010)
J Biol Inorg Chem
, vol.15
, pp. 689-700
-
-
Sinibaldi, F.1
Howes, B.D.2
Piro, M.C.3
Polticelli, F.4
Bombelli, C.5
Ferri, T.6
Coletta, M.7
Smulevich, G.8
Santucci, R.9
-
22
-
-
76249087938
-
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
-
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, and Vorobyov I et al. (2010) CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31:671-690.
-
(2010)
J Comput Chem
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
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