-
1
-
-
33847076849
-
Chromatin Modifications and Their Function
-
Kouzarides, T. Chromatin Modifications and Their Function Cell 2007, 128, 693-705 10.1016/j.cell.2007.02.005
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
2
-
-
84860371953
-
Epigenetic Protein Families: A New Frontier for Drug Discovery
-
Arrowsmith, C. H.; Bountra, C.; Fish, P. V.; Lee, K.; Schapira, M. Epigenetic Protein Families: A New Frontier for Drug Discovery Nat. Rev. Drug Discovery 2012, 11, 384-400 10.1038/nrd3674
-
(2012)
Nat. Rev. Drug Discovery
, vol.11
, pp. 384-400
-
-
Arrowsmith, C.H.1
Bountra, C.2
Fish, P.V.3
Lee, K.4
Schapira, M.5
-
3
-
-
79955856345
-
Therapeutic Prospects for Epigenetic Modulation
-
Heightman, T. D. Therapeutic Prospects for Epigenetic Modulation Expert Opin. Ther. Targets 2011, 15, 729-740 10.1517/14728222.2011.561786
-
(2011)
Expert Opin. Ther. Targets
, vol.15
, pp. 729-740
-
-
Heightman, T.D.1
-
4
-
-
79955665883
-
Bromodomain Coactivators in Cancer, Obesity, Type 2 Diabetes, and Inflammation
-
Denis, G. V. Bromodomain Coactivators in Cancer, Obesity, Type 2 Diabetes, and Inflammation Discovery Med. 2010, 10 (55) 489-499
-
(2010)
Discovery Med.
, vol.10
, Issue.55
, pp. 489-499
-
-
Denis, G.V.1
-
5
-
-
70149105669
-
The Role of Human Bromodomains in Chromatin Biology and Gene Transcription
-
Sanchez, R.; Zhou, M. M. The Role of Human Bromodomains in Chromatin Biology and Gene Transcription Curr. Opin. Drug Disc. 2009, 12, 659-665
-
(2009)
Curr. Opin. Drug Disc.
, vol.12
, pp. 659-665
-
-
Sanchez, R.1
Zhou, M.M.2
-
6
-
-
79952534189
-
Regulation of Chromatin by Histone Modifications
-
Bannister, A. J.; Kouzarides, T. Regulation of Chromatin by Histone Modifications Cell Res. 2011, 21, 381-395 10.1038/cr.2011.22
-
(2011)
Cell Res.
, vol.21
, pp. 381-395
-
-
Bannister, A.J.1
Kouzarides, T.2
-
7
-
-
84860371870
-
Combinatorial Complexity in Chromatin Structure and Function: Revisiting the Histone Code
-
Rando, O. J. Combinatorial Complexity in Chromatin Structure and Function: Revisiting The Histone Code Curr. Opin. Genet. Dev. 2012, 22, 148-155 10.1016/j.gde.2012.02.013
-
(2012)
Curr. Opin. Genet. Dev.
, vol.22
, pp. 148-155
-
-
Rando, O.J.1
-
8
-
-
15044358494
-
Reading Signals on the Nucleosome with A New Nomenclature for Modified Histones
-
Turner, B. M. Reading Signals on The Nucleosome with A New Nomenclature for Modified Histones Nat. Struct. Mol. Biol. 2005, 12, 110-112 10.1038/nsmb0205-110
-
(2005)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 110-112
-
-
Turner, B.M.1
-
9
-
-
0035839136
-
Translating the Histone Code
-
Jenuwein, T.; Allis, C. D. Translating The Histone Code Science 2001, 293, 1074-1080 10.1126/science.1063127
-
(2001)
Science
, vol.293
, pp. 1074-1080
-
-
Jenuwein, T.1
Allis, C.D.2
-
10
-
-
84859731822
-
Epigenetic Modifications in Cardiovascular Disease
-
Lorenzen, J. M.; Martino, F.; Thum, T. Epigenetic Modifications In Cardiovascular Disease Basic Res. Cardiol. 2012, 107, 1-10 10.1007/s00395-012-0245-9
-
(2012)
Basic Res. Cardiol.
, vol.107
, pp. 1-10
-
-
Lorenzen, J.M.1
Martino, F.2
Thum, T.3
-
11
-
-
84860371953
-
Epigenetic Protein Families: A New Frontier for Drug Discovery
-
Arrowsmith, C. H.; Bountra, C.; Fish, P. V.; Lee, K.; Schapira, M. Epigenetic Protein Families: A New Frontier for Drug Discovery Nat. Rev. Drug Discovery 2012, 11, 384-400 10.1038/nrd3674
-
(2012)
Nat. Rev. Drug Discovery
, vol.11
, pp. 384-400
-
-
Arrowsmith, C.H.1
Bountra, C.2
Fish, P.V.3
Lee, K.4
Schapira, M.5
-
12
-
-
84863621527
-
Cancer Epigenetics: From Mechanism to Therapy
-
Dawson, M. A.; Kouzarides, T. Cancer Epigenetics: From Mechanism to Therapy Cell 2012, 150, 12-27 10.1016/j.cell.2012.06.013
-
(2012)
Cell
, vol.150
, pp. 12-27
-
-
Dawson, M.A.1
Kouzarides, T.2
-
13
-
-
77953995002
-
Covalent Histone Modifications - Miswritten, Misinterpreted and Mis-Erased in Human Cancers
-
Chi, P.; Allis, C. D.; Wang, G. G. Covalent Histone Modifications-Miswritten, Misinterpreted and Mis-Erased in Human Cancers Nat. Rev. Cancer 2010, 10, 457-469 10.1038/nrc2876
-
(2010)
Nat. Rev. Cancer
, vol.10
, pp. 457-469
-
-
Chi, P.1
Allis, C.D.2
Wang, G.G.3
-
14
-
-
0033519641
-
Structure and Ligand of A Histone Acetyltransferase Bromodomain
-
Dhalluin, C.; Carlson, J. E.; Zeng, L.; He, C.; Aggarwal, A. K.; Zhou, M. M. Structure and Ligand of A Histone Acetyltransferase Bromodomain Nature 1999, 399, 491-496 10.1038/20974
-
(1999)
Nature
, vol.399
, pp. 491-496
-
-
Dhalluin, C.1
Carlson, J.E.2
Zeng, L.3
He, C.4
Aggarwal, A.K.5
Zhou, M.M.6
-
15
-
-
84857331171
-
Inhibition of Bromodomain-Mediated Protein-Protein Interactions as A Novel Therapeutic Strategy
-
Furdas, S. D.; Carlino, L.; Sippl, W.; Jung, M. Inhibition of Bromodomain-Mediated Protein-Protein Interactions as A Novel Therapeutic Strategy MedChemComm 2012, 3, 123-134 10.1039/C1MD00201E
-
(2012)
MedChemComm
, vol.3
, pp. 123-134
-
-
Furdas, S.D.1
Carlino, L.2
Sippl, W.3
Jung, M.4
-
16
-
-
84859181036
-
Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family
-
Filippakopoulos, P.; Picaud, S.; Mangos, M.; Keates, T.; Lambert, J. P.; Barsyte-Lovejoy, D.; Felletar, I.; Volkmer, R.; Muller, S.; Pawson, T.; Gingras, A. C.; Arrowsmith, C. H.; Knapp, S. Histone Recognition and Large-Scale Structural Analysis of The Human Bromodomain Family Cell 2012, 149, 214-231 10.1016/j.cell.2012.02.013
-
(2012)
Cell
, vol.149
, pp. 214-231
-
-
Filippakopoulos, P.1
Picaud, S.2
Mangos, M.3
Keates, T.4
Lambert, J.P.5
Barsyte-Lovejoy, D.6
Felletar, I.7
Volkmer, R.8
Muller, S.9
Pawson, T.10
Gingras, A.C.11
Arrowsmith, C.H.12
Knapp, S.13
-
17
-
-
84905269946
-
Structure-Based Virtual Screening of Novel, High-Affinity BRD4 Inhibitors
-
Muvva, C.; Singam, E. R. A.; Raman, S. S.; Subramanian, V. Structure-Based Virtual Screening of Novel, High-Affinity BRD4 Inhibitors Mol. BioSyst. 2014, 10, 2384-2397 10.1039/C4MB00243A
-
(2014)
Mol. BioSyst.
, vol.10
, pp. 2384-2397
-
-
Muvva, C.1
Singam, E.R.A.2
Raman, S.S.3
Subramanian, V.4
-
18
-
-
84899934825
-
Discovery of BRD4 Bromodomain Inhibitors by Fragment-Based High-Throughput Docking
-
Zhao, H. T.; Gartenmann, L.; Dong, J.; Spiliotopoulos, D.; Caflisch, A. Discovery of BRD4 Bromodomain Inhibitors by Fragment-Based High-Throughput Docking Bioorg. Med. Chem. Lett. 2014, 24, 2493-2496 10.1016/j.bmcl.2014.04.017
-
(2014)
Bioorg. Med. Chem. Lett.
, vol.24
, pp. 2493-2496
-
-
Zhao, H.T.1
Gartenmann, L.2
Dong, J.3
Spiliotopoulos, D.4
Caflisch, A.5
-
19
-
-
84870013141
-
Progress in the Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions
-
Hewings, D. S.; Rooney, T. P. C.; Jennings, L. E.; Hay, D. A.; Schofield, C. J.; Brennan, P. E.; Knapp, S.; Conway, S. J. Progress in The Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions J. Med. Chem. 2012, 55, 9393-9413 10.1021/jm300915b
-
(2012)
J. Med. Chem.
, vol.55
, pp. 9393-9413
-
-
Hewings, D.S.1
Rooney, T.P.C.2
Jennings, L.E.3
Hay, D.A.4
Schofield, C.J.5
Brennan, P.E.6
Knapp, S.7
Conway, S.J.8
-
20
-
-
84856394571
-
Bromodomains as Therapeutic Targets
-
Muller, S.; Filippakopoulos, P.; Knapp, S. Bromodomains as Therapeutic Targets Expert Rev. Mol. Med. 2011, 13, 1-21 10.1017/S1462399411001992
-
(2011)
Expert Rev. Mol. Med.
, vol.13
, pp. 1-21
-
-
Muller, S.1
Filippakopoulos, P.2
Knapp, S.3
-
21
-
-
80054984945
-
Inhibition of Bet Recruitment to Chromatin as An Effective Treatment for Mll-Fusion Leukaemia
-
Dawson, M. A.; Prinjha, R. K.; Dittmann, A.; Giotopoulos, G.; Bantscheff, M.; Chan, W. I.; Robson, S. C.; Chung, C. W.; Hopf, C.; Savitski, M. M.; Huthmacher, C.; Gudgin, E.; Lugo, D.; Beinke, S.; Chapman, T. D.; Roberts, E. J.; Soden, P. E.; Auger, K. R.; Mirguet, O.; Doehner, K.; Delwel, R.; Burnett, A. K.; Jeffrey, P.; Drewes, G.; Lee, K.; Huntly, B. J. P.; Kouzarides, T. Inhibition of Bet Recruitment to Chromatin as An Effective Treatment for Mll-Fusion Leukaemia Nature 2011, 478, 529-533 10.1038/nature10509
-
(2011)
Nature
, vol.478
, pp. 529-533
-
-
Dawson, M.A.1
Prinjha, R.K.2
Dittmann, A.3
Giotopoulos, G.4
Bantscheff, M.5
Chan, W.I.6
Robson, S.C.7
Chung, C.W.8
Hopf, C.9
Savitski, M.M.10
Huthmacher, C.11
Gudgin, E.12
Lugo, D.13
Beinke, S.14
Chapman, T.D.15
Roberts, E.J.16
Soden, P.E.17
Auger, K.R.18
Mirguet, O.19
Doehner, K.20
Delwel, R.21
Burnett, A.K.22
Jeffrey, P.23
Drewes, G.24
Lee, K.25
Huntly, B.J.P.26
Kouzarides, T.27
more..
-
22
-
-
80052955256
-
BET Bromodomain Inhibition as A Therapeutic Strategy to Target C-Myc
-
Delmore, J. E.; Issa, G. C.; Lemieux, M. E.; Rahl, P. B.; Shi, J. W.; Jacobs, H. M.; Kastritis, E.; Gilpatrick, T.; Paranal, R. M.; Qi, J.; Chesi, M.; Schinzel, A. C.; Mckeown, M. R.; Heffernan, T. P.; Vakoc, C. R.; Bergsagel, P. L.; Ghobrial, I. M.; Richardson, P. G.; Young, R. A.; Hahn, W. C.; Anderson, K. C.; Kung, A. L.; Bradner, J. E.; Mitsiades, C. S. BET Bromodomain Inhibition as A Therapeutic Strategy to Target C-Myc Cell 2011, 146, 904-917 10.1016/j.cell.2011.08.017
-
(2011)
Cell
, vol.146
, pp. 904-917
-
-
Delmore, J.E.1
Issa, G.C.2
Lemieux, M.E.3
Rahl, P.B.4
Shi, J.W.5
Jacobs, H.M.6
Kastritis, E.7
Gilpatrick, T.8
Paranal, R.M.9
Qi, J.10
Chesi, M.11
Schinzel, A.C.12
McKeown, M.R.13
Heffernan, T.P.14
Vakoc, C.R.15
Bergsagel, P.L.16
Ghobrial, I.M.17
Richardson, P.G.18
Young, R.A.19
Hahn, W.C.20
Anderson, K.C.21
Kung, A.L.22
Bradner, J.E.23
Mitsiades, C.S.24
more..
-
23
-
-
78650847770
-
Selective Inhibition of BET Bromodomains
-
Filippakopoulos, P.; Qi, J.; Picaud, S.; Shen, Y.; Smith, W. B.; Fedorov, O.; Morse, E. M.; Keates, T.; Hickman, T. T.; Felletar, I.; Philpott, M.; Munro, S.; Mckeown, M. R.; Wang, Y.; Christie, A. L.; West, N.; Cameron, M. J.; Schwartz, B.; Heightman, T. D.; La Thangue, N.; French, C. A.; Wiest, O.; Kung, A. L.; Knapp, S.; Bradner, J. E. Selective Inhibition of BET Bromodomains Nature 2010, 468, 1067-1073 10.1038/nature09504
-
(2010)
Nature
, vol.468
, pp. 1067-1073
-
-
Filippakopoulos, P.1
Qi, J.2
Picaud, S.3
Shen, Y.4
Smith, W.B.5
Fedorov, O.6
Morse, E.M.7
Keates, T.8
Hickman, T.T.9
Felletar, I.10
Philpott, M.11
Munro, S.12
McKeown, M.R.13
Wang, Y.14
Christie, A.L.15
West, N.16
Cameron, M.J.17
Schwartz, B.18
Heightman, T.D.19
La Thangue, N.20
French, C.A.21
Wiest, O.22
Kung, A.L.23
Knapp, S.24
Bradner, J.E.25
more..
-
24
-
-
80053651202
-
Targeting Myc Dependence in Cancer by Inhibiting BET Bromodomains
-
Mertz, J. A.; Conery, A. R.; Bryant, B. M.; Sandy, P.; Balasubramanian, S.; Mele, D. A.; Bergeron, L.; Sims, R. J. Targeting Myc Dependence in Cancer by Inhibiting BET Bromodomains Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 16669-16674 10.1073/pnas.1108190108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 16669-16674
-
-
Mertz, J.A.1
Conery, A.R.2
Bryant, B.M.3
Sandy, P.4
Balasubramanian, S.5
Mele, D.A.6
Bergeron, L.7
Sims, R.J.8
-
25
-
-
78650806593
-
Suppression of Inflammation by A Synthetic Histone Mimic
-
Nicodeme, E.; Jeffrey, K. L.; Schaefer, U.; Beinke, S.; Dewell, S.; Chung, C. W.; Chandwani, R.; Marazzi, I.; Wilson, P.; Coste, H.; White, J.; Kirilovsky, J.; Rice, C. M.; Lora, J. M.; Prinjha, R. K.; Lee, K.; Tarakhovsky, A. Suppression of Inflammation by A Synthetic Histone Mimic Nature 2010, 468, 1119-1123 10.1038/nature09589
-
(2010)
Nature
, vol.468
, pp. 1119-1123
-
-
Nicodeme, E.1
Jeffrey, K.L.2
Schaefer, U.3
Beinke, S.4
Dewell, S.5
Chung, C.W.6
Chandwani, R.7
Marazzi, I.8
Wilson, P.9
Coste, H.10
White, J.11
Kirilovsky, J.12
Rice, C.M.13
Lora, J.M.14
Prinjha, R.K.15
Lee, K.16
Tarakhovsky, A.17
-
26
-
-
84879692312
-
Does Bromodomain Flexibility Influence Histone Recognition?
-
Steiner, S.; Magno, A.; Huang, D.; Caflisch, A. Does Bromodomain Flexibility Influence Histone Recognition? FEBS Lett. 2013, 587, 2158-63 10.1016/j.febslet.2013.05.032
-
(2013)
FEBS Lett.
, vol.587
, pp. 2158-2163
-
-
Steiner, S.1
Magno, A.2
Huang, D.3
Caflisch, A.4
-
27
-
-
33748518255
-
Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins: Struct., Funct., Genet. 2006, 65, 712-725 10.1002/prot.21123
-
(2006)
Proteins: Struct., Funct., Genet.
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
28
-
-
2942532422
-
Development and Testing of A General Amber Force Field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of A General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174 10.1002/jcc.20035
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
29
-
-
3042524904
-
A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges the Resp Model
-
Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges The Resp Model J. Phys. Chem. 1993, 97, 10269-10280 10.1021/j100142a004
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
30
-
-
70450206724
-
-
Gaussian. Inc: Wallingford CT
-
Frisch, M. J.; T, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, Gaussian. Inc: Wallingford CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.T.G.W.1
Schlegel, H.B.2
Scuseria, G.E.3
Robb, M.A.4
Cheeseman, J.R.5
Scalmani, G.6
Barone, V.7
Mennucci, B.8
Petersson, G.A.9
Nakatsuji, H.10
Caricato, M.11
Li, X.12
Hratchian, H.P.13
Izmaylov, A.F.14
Bloino, J.15
Zheng, G.16
Sonnenberg, J.L.17
Hada, M.18
Ehara, M.19
Toyota, K.20
Fukuda, R.21
Hasegawa, J.22
Ishida, M.23
Nakajima, T.24
Honda, Y.25
Kitao, O.26
Nakai, H.27
Vreven, T.28
Montgomery, J.A.29
Peralta, J.E.30
Ogliaro, F.31
Bearpark, M.32
Heyd, J.J.33
Brothers, E.34
Kudin, K.N.35
Staroverov, V.N.36
Kobayashi, R.37
Normand, J.38
Raghavachari, K.39
Rendell, A.40
Burant, J.C.41
Iyengar, S.S.42
Tomasi, J.43
Cossi, M.44
Rega, N.45
Millam, J.M.46
Klene, M.47
Knox, J.E.48
Cross, J.B.49
Bakken, V.50
Adamo, C.51
Jaramillo, J.52
Gomperts, R.53
Stratmann, R.E.54
Yazyev, O.55
Austin, A.J.56
Cammi, R.57
Pomelli, C.58
Ochterski, J.W.59
Martin, R.L.60
Morokuma, K.61
Zakrzewski, V.G.62
Voth, G.A.63
Salvador, P.64
Dannenberg, J.J.65
Dapprich, S.66
Daniels, A.D.67
Farkas, O.68
Foresman, J.B.69
Ortiz, J.V.70
Cioslowski, J.71
Fox, D.J.72
more..
-
31
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935 10.1063/1.445869
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
32
-
-
23444454552
-
The Amber Biomolecular Simulation Programs
-
Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26, 1668-1688 10.1002/jcc.20290
-
(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
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
33
-
-
33750587438
-
Molecular Dynamics with Coupling to An External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular Dynamics with Coupling to An External Bath J. Chem. Phys. 1984, 81, 3684 10.1063/1.448118
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
34
-
-
33646940952
-
Numerical Integration of the Cartesian Equations of Motion of A System with Constraints: Molecular Dynamics of N-Alkanes
-
Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of The Cartesian Equations of Motion of A System with Constraints: Molecular Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327-341 10.1016/0021-9991(77)90098-5
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
35
-
-
84871864524
-
Molecular Dynamics and Umbrella Sampling Study of Stabilizing Factors in Cyclic Peptide-Based Nanotubes
-
Vijayaraj, R.; Van Damme, S.; Bultinck, P.; Subramanian, V. Molecular Dynamics and Umbrella Sampling Study of Stabilizing Factors in Cyclic Peptide-Based Nanotubes J. Phys. Chem. B 2012, 116, 9922-9933 10.1021/jp303418a
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 9922-9933
-
-
Vijayaraj, R.1
Van Damme, S.2
Bultinck, P.3
Subramanian, V.4
-
37
-
-
79960707811
-
Characterizing the Dynamics and Ligand-Specific Interactions in the Human Leukocyte Elastase Through Molecular Dynamics Simulations
-
Estacio, S. G.; Moreira, R.; Guedes, R. C. Characterizing The Dynamics and Ligand-Specific Interactions in The Human Leukocyte Elastase Through Molecular Dynamics Simulations J. Chem. Inf. Model. 2011, 51, 1690-1702 10.1021/ci200076k
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1690-1702
-
-
Estacio, S.G.1
Moreira, R.2
Guedes, R.C.3
-
38
-
-
79960337244
-
Mechanism of 150-Cavity Formation in Influenza Neuraminidase
-
Amaro, R. E.; Swift, R. V.; Votapka, L.; Li, W. W.; Walker, R. C.; Bush, R. M. Mechanism of 150-Cavity Formation in Influenza Neuraminidase Nat. Commun. 2011, 2, 388 10.1038/ncomms1390
-
(2011)
Nat. Commun.
, vol.2
, pp. 388
-
-
Amaro, R.E.1
Swift, R.V.2
Votapka, L.3
Li, W.W.4
Walker, R.C.5
Bush, R.M.6
-
39
-
-
45849120595
-
Understanding Ligand-Based Modulation of the Hsp90 Molecular Chaperone Dynamics at Atomic Resolution
-
Colombo, G.; Morra, G.; Meli, M.; Verkhivker, G. Understanding Ligand-Based Modulation of The Hsp90 Molecular Chaperone Dynamics at Atomic Resolution Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 7976-7981 10.1073/pnas.0802879105
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 7976-7981
-
-
Colombo, G.1
Morra, G.2
Meli, M.3
Verkhivker, G.4
-
40
-
-
36649006642
-
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
-
Shao, J. Y.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. Clustering Molecular Dynamics Trajectories: 1. Characterizing The Performance of Different Clustering Algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334 10.1021/ct700119m
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2312-2334
-
-
Shao, J.Y.1
Tanner, S.W.2
Thompson, N.3
Cheatham, T.E.4
-
41
-
-
79751535059
-
Povme: An Algorithm for Measuring Binding-Pocket Volumes
-
Durrant, J. D.; De Oliveira, C. A. F.; Mccammon, J. A. Povme: An Algorithm for Measuring Binding-Pocket Volumes J. Mol. Graphics Modell. 2011, 29, 773-776 10.1016/j.jmgm.2010.10.007
-
(2011)
J. Mol. Graphics Modell.
, vol.29
, pp. 773-776
-
-
Durrant, J.D.1
De Oliveira, C.A.F.2
McCammon, J.A.3
-
42
-
-
79955574923
-
-
Version 1.6; Schrödinger Llc: New York
-
The Pymol Molecular Graphics System. Version 1.6; Schrödinger Llc: New York, 2013.
-
(2013)
The Pymol Molecular Graphics System
-
-
-
43
-
-
0345491105
-
Development of the Colle-Salvetti Correlation-Energy Formula into A Functional of the Electron Density
-
Lee, C.; Yang, W.; Parr, R. G. Development of The Colle-Salvetti Correlation-Energy Formula Into A Functional of The Electron Density Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
-
(1988)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
44
-
-
4243553426
-
Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior
-
Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
-
(1988)
Phys. Rev. A: At., Mol., Opt. Phys.
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
45
-
-
33748263629
-
Pseudobond Ab Initio Qm/Mm Approach and Its Applications to Enzyme Reactions
-
Zhang, Y. K. Pseudobond Ab Initio Qm/Mm Approach and Its Applications to Enzyme Reactions Theor. Chem. Acc. 2006, 116, 43-50 10.1007/s00214-005-0008-x
-
(2006)
Theor. Chem. Acc.
, vol.116
, pp. 43-50
-
-
Zhang, Y.K.1
-
46
-
-
22944472113
-
Improved Pseudobonds for Combined Ab Initio Quantum Mechanical/Molecular Mechanical Methods
-
Zhang, Y. K. Improved Pseudobonds for Combined Ab Initio Quantum Mechanical/Molecular Mechanical Methods J. Chem. Phys. 2005, 122, 024114 10.1063/1.1834899
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 024114
-
-
Zhang, Y.K.1
-
47
-
-
0000145441
-
Free Energy Calculation on Enzyme Reactions with An Efficient Iterative Procedure to Determine Minimum Energy Paths on A Combined Ab Initio Qm/Mm Potential Energy Surface
-
Zhang, Y. K.; Liu, H. Y.; Yang, W. T. Free Energy Calculation on Enzyme Reactions with An Efficient Iterative Procedure to Determine Minimum Energy Paths on A Combined Ab Initio Qm/Mm Potential Energy Surface J. Chem. Phys. 2000, 112, 3483-3492 10.1063/1.480503
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 3483-3492
-
-
Zhang, Y.K.1
Liu, H.Y.2
Yang, W.T.3
-
48
-
-
0001582558
-
A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods
-
Zhang, Y. K.; Lee, T. S.; Yang, W. T. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods J. Chem. Phys. 1999, 110, 46-54 10.1063/1.478083
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 46-54
-
-
Zhang, Y.K.1
Lee, T.S.2
Yang, W.T.3
-
49
-
-
0000394426
-
Some Multistep Methods for Use in Molecular Dynamics Calculations
-
Beeman, D. Some Multistep Methods for Use In Molecular Dynamics Calculations J. Comput. Phys. 1976, 20, 130-139 10.1016/0021-9991(76)90059-0
-
(1976)
J. Comput. Phys.
, vol.20
, pp. 130-139
-
-
Beeman, D.1
-
50
-
-
70349299369
-
-
Q-chem,Inc. Pittsburgh,PA
-
Shao, Y.; M, L. F.; Jung, Y.; Kussmann, J. O. C.; Brown, S. T.; Gilbert, A. T.; Slipchenko, L. V.; Levchenko, S. V.; O'neill, D. P.; Distasio, R. A.; Lochan, R. C.; Wang, T.; Beran, G. J.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C. P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L.; Zhang, W.; Bell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F.; Kong, J.; Krylov, A. I.; Gill, P. M.; Head-Gordon, M. Q-Chem,Version 3.0, Q-chem,Inc.: Pittsburgh,PA. 2006.
-
(2006)
Q-Chem, Version 3.0
-
-
Shao, Y.1
Jung, Y.2
Kussmann, J.O.C.3
Brown, S.T.4
Gilbert, A.T.5
Slipchenko, L.V.6
Levchenko, S.V.7
O'Neill, D.P.8
Distasio, R.A.9
Lochan, R.C.10
Wang, T.11
Beran, G.J.12
Besley, N.A.13
Herbert, J.M.14
Lin, C.Y.15
Van Voorhis, T.16
Chien, S.H.17
Sodt, A.18
Steele, R.P.19
Rassolov, V.A.20
Maslen, P.E.21
Korambath, P.P.22
Adamson, R.D.23
Austin, B.24
Baker, J.25
Byrd, E.F.26
Dachsel, H.27
Doerksen, R.J.28
Dreuw, A.29
Dunietz, B.D.30
Dutoi, A.D.31
Furlani, T.R.32
Gwaltney, S.R.33
Heyden, A.34
Hirata, S.35
Hsu, C.P.36
Kedziora, G.37
Khalliulin, R.Z.38
Klunzinger, P.39
Lee, A.M.40
Lee, M.S.41
Liang, W.42
Lotan, I.43
Nair, N.44
Peters, B.45
Proynov, E.I.46
Pieniazek, P.A.47
Rhee, Y.M.48
Ritchie, J.49
Rosta, E.50
Sherrill, C.D.51
Simmonett, A.C.52
Subotnik, J.E.53
Woodcock, H.L.54
Zhang, W.55
Bell, A.T.56
Chakraborty, A.K.57
Chipman, D.M.58
Keil, F.J.59
Warshel, A.60
Hehre, W.J.61
Schaefer, H.F.62
Kong, J.63
Krylov, A.I.64
Gill, P.M.65
Head-Gordon, M.66
more..
-
52
-
-
84863165405
-
Qm/Mm Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase
-
Wu, R. B.; Gong, W. J.; Liu, T.; Zhang, Y. K.; Cao, Z. X. Qm/Mm Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase J. Phys. Chem. B 2012, 116, 1984-1991 10.1021/jp211403j
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 1984-1991
-
-
Wu, R.B.1
Gong, W.J.2
Liu, T.3
Zhang, Y.K.4
Cao, Z.X.5
-
53
-
-
79954998200
-
Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel
-
Wu, R. B.; Lu, Z. Y.; Cao, Z. X.; Zhang, Y. K. Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to The Linker Binding Channel J. Am. Chem. Soc. 2011, 133, 6110-6113 10.1021/ja111104p
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 6110-6113
-
-
Wu, R.B.1
Lu, Z.Y.2
Cao, Z.X.3
Zhang, Y.K.4
-
54
-
-
84913581030
-
Structure-Function Analysis of the Conserved Tyrosine and Diverse Pi-Stacking among Class i Histone Deacetylases: A Qm (DFT)/Mm Md Study
-
Zhou, J. W.; Xie, H. J.; Liu, Z. H.; Luo, H. B.; Wu, R. B. Structure-Function Analysis of The Conserved Tyrosine and Diverse Pi-Stacking Among Class I Histone Deacetylases: A Qm (Dft)/Mm Md Study J. Chem. Inf. Model. 2014, 54, 3162-3171 10.1021/ci500513n
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 3162-3171
-
-
Zhou, J.W.1
Xie, H.J.2
Liu, Z.H.3
Luo, H.B.4
Wu, R.B.5
-
55
-
-
84896262993
-
Concerted Cyclization of Lanosterol C-Ring and D-Ring under Human Oxidosqualene Cyclase Catalysis: An Ab Initio Qm/Mm Md Study
-
Chen, N. H.; Zhou, J. W.; Li, J. B.; Xu, J.; Wu, R. B. Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An Ab Initio Qm/Mm Md Study J. Chem. Theory Comput. 2014, 10, 1109-1120 10.1021/ct400949b
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1109-1120
-
-
Chen, N.H.1
Zhou, J.W.2
Li, J.B.3
Xu, J.4
Wu, R.B.5
-
56
-
-
84921284940
-
Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions
-
Brand, M.; Measures, A. M.; Wilson, B. G.; Cortopassi, W. A.; Alexander, R.; Hoss, M.; Hewings, D. S.; Rooney, T. P. C.; Paton, R. S.; Conway, S. J. Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions ACS Chem. Biol. 2015, 10, 22-39 10.1021/cb500996u
-
(2015)
ACS Chem. Biol.
, vol.10
, pp. 22-39
-
-
Brand, M.1
Measures, A.M.2
Wilson, B.G.3
Cortopassi, W.A.4
Alexander, R.5
Hoss, M.6
Hewings, D.S.7
Rooney, T.P.C.8
Paton, R.S.9
Conway, S.J.10
-
57
-
-
84889663966
-
Rvx-208, An Inhibitor of BET Transcriptional Regulators with Selectivity for the Second Bromodomain
-
Picaud, S.; Wells, C.; Felletar, I.; Brotherton, D.; Martin, S.; Savitsky, P.; Diez-Dacal, B.; Philpott, M.; Bountra, C.; Lingard, H.; Fedorov, O.; Muller, S.; Brennan, P. E.; Knapp, S.; Filippakopoulos, P. Rvx-208, An Inhibitor of BET Transcriptional Regulators with Selectivity for The Second Bromodomain Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 19754-19759 10.1073/pnas.1310658110
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 19754-19759
-
-
Picaud, S.1
Wells, C.2
Felletar, I.3
Brotherton, D.4
Martin, S.5
Savitsky, P.6
Diez-Dacal, B.7
Philpott, M.8
Bountra, C.9
Lingard, H.10
Fedorov, O.11
Muller, S.12
Brennan, P.E.13
Knapp, S.14
Filippakopoulos, P.15
-
58
-
-
77958535230
-
Binding Kinetics and Mechanism of Action: Toward the Discovery and Development of Better and Best in Class Drugs
-
Zhang, R.; Monsma, F. Binding Kinetics and Mechanism of Action: Toward The Discovery and Development of Better and Best in Class Drugs Expert Opin. Drug Discovery 2010, 5, 1023-1029 10.1517/17460441.2010.520700
-
(2010)
Expert Opin. Drug Discovery
, vol.5
, pp. 1023-1029
-
-
Zhang, R.1
Monsma, F.2
-
59
-
-
84875016493
-
Free Energy Landscape for the Binding Process of Huperzine A to Acetylcholinesterase
-
Bai, F.; Xu, Y.; Chen, J.; Liu, Q.; Gu, J.; Wang, X.; Ma, J.; Li, H.; Onuchic, J. N.; Jiang, H. Free Energy Landscape for The Binding Process of Huperzine A to Acetylcholinesterase Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 4273-4278 10.1073/pnas.1301814110
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 4273-4278
-
-
Bai, F.1
Xu, Y.2
Chen, J.3
Liu, Q.4
Gu, J.5
Wang, X.6
Ma, J.7
Li, H.8
Onuchic, J.N.9
Jiang, H.10
-
60
-
-
84893699626
-
Divergent Kinetics Differentiate the Mechanism of Action of Two Hdac Inhibitors
-
Kral, A. M.; Ozerova, N.; Close, J.; Jung, J.; Chenard, M.; Fleming, J.; Haines, B. B.; Harrington, P.; Maclean, J.; Miller, T. A.; Secrist, P.; Wang, H.; Heidebrecht, R. J. Divergent Kinetics Differentiate The Mechanism of Action of Two Hdac Inhibitors Biochemistry 2014, 53, 725-734 10.1021/bi400936h
-
(2014)
Biochemistry
, vol.53
, pp. 725-734
-
-
Kral, A.M.1
Ozerova, N.2
Close, J.3
Jung, J.4
Chenard, M.5
Fleming, J.6
Haines, B.B.7
Harrington, P.8
Maclean, J.9
Miller, T.A.10
Secrist, P.11
Wang, H.12
Heidebrecht, R.J.13
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