-
1
-
-
0035716744
-
Hsp70 Chaperone Machines
-
Mayer, M. P.; Brehmer, D.; Gässler, C. S.; Bukau, B. Hsp70 Chaperone Machines Adv. Protein Chem. 2001, 59, 1-44 10.1016/S0065-3233(01)59001-4
-
(2001)
Adv. Protein Chem.
, vol.59
, pp. 1-44
-
-
Mayer, M.P.1
Brehmer, D.2
Gässler, C.S.3
Bukau, B.4
-
2
-
-
79960652801
-
Molecular Chaperones in Protein Folding and Proteostasis
-
Hartl, F. U.; Bracher, A.; Hayer-Hartl, M. Molecular Chaperones in Protein Folding and Proteostasis Nature 2011, 475, 324-332 10.1038/nature10317
-
(2011)
Nature
, vol.475
, pp. 324-332
-
-
Hartl, F.U.1
Bracher, A.2
Hayer-Hartl, M.3
-
3
-
-
84878948560
-
Molecular Chaperone Functions in Protein Folding and Proteostasis
-
Kim, Y. E.; Hipp, M. S.; Bracher, A.; Hayer-Hartl, M.; Hartl, F. U. Molecular Chaperone Functions in Protein Folding and Proteostasis Annu. Rev. Biochem. 2013, 82, 323-355 10.1146/annurev-biochem-060208-092442
-
(2013)
Annu. Rev. Biochem.
, vol.82
, pp. 323-355
-
-
Kim, Y.E.1
Hipp, M.S.2
Bracher, A.3
Hayer-Hartl, M.4
Hartl, F.U.5
-
4
-
-
84886412961
-
Chaperone Machines for Protein Folding, Unfolding and Disaggregation
-
Saibil, H. Chaperone Machines for Protein Folding, Unfolding and Disaggregation Nat. Rev. Mol. Cell Biol. 2013, 14, 630-642 10.1038/nrm3658
-
(2013)
Nat. Rev. Mol. Cell Biol.
, vol.14
, pp. 630-642
-
-
Saibil, H.1
-
5
-
-
17044387386
-
Hsp70 Chaperones: Cellular Functions and Molecular Mechanism
-
Mayer, M. P.; Bukau, B. Hsp70 Chaperones: Cellular Functions and Molecular Mechanism Cell. Mol. Life Sci. 2005, 62, 670-684 10.1007/s00018-004-4464-6
-
(2005)
Cell. Mol. Life Sci.
, vol.62
, pp. 670-684
-
-
Mayer, M.P.1
Bukau, B.2
-
6
-
-
84884589727
-
Hsp70 Chaperone Dynamics and Molecular Mechanism
-
Mayer, M. P. Hsp70 Chaperone Dynamics and Molecular Mechanism Trends Biochem. Sci. 2013, 38, 507-514 10.1016/j.tibs.2013.08.001
-
(2013)
Trends Biochem. Sci.
, vol.38
, pp. 507-514
-
-
Mayer, M.P.1
-
7
-
-
84874473589
-
Allostery in the Hsp70 Chaperone Proteins
-
Zuiderweg, E. R.; Bertelsen, E. B.; Rousaki, A.; Mayer, M. P.; Gestwicki, J. E.; Ahmad, A. Allostery in the Hsp70 Chaperone Proteins Top. Curr. Chem. 2012, 328, 99-153 10.1007/128-2012-323
-
(2012)
Top. Curr. Chem.
, vol.328
, pp. 99-153
-
-
Zuiderweg, E.R.1
Bertelsen, E.B.2
Rousaki, A.3
Mayer, M.P.4
Gestwicki, J.E.5
Ahmad, A.6
-
8
-
-
0035182221
-
Stress Management - Heat Shock Protein-70 and the Regulation of Apoptosis
-
Beere, H. M.; Green, D. R. Stress Management-Heat Shock Protein-70 and the Regulation of Apoptosis Trends Cell Biol. 2001, 11, 6-10 10.1016/S0962-8924(00)01874-2
-
(2001)
Trends Cell Biol.
, vol.11
, pp. 6-10
-
-
Beere, H.M.1
Green, D.R.2
-
9
-
-
33746364784
-
Structure and Mechanism of the Hsp90 Molecular Chaperone Machinery
-
Pearl, L. H.; Prodromou, C. Structure and Mechanism of the Hsp90 Molecular Chaperone Machinery Annu. Rev. Biochem. 2006, 75, 271-294 10.1146/annurev.biochem.75.103004.142738
-
(2006)
Annu. Rev. Biochem.
, vol.75
, pp. 271-294
-
-
Pearl, L.H.1
Prodromou, C.2
-
10
-
-
34848926209
-
Diverse Cellular Functions of the Hsp90 Molecular Chaperone Uncovered Using Systems Approaches
-
McClellan, A. J.; Xia, Y.; Deutschbauer, A. M.; Davis, R. W.; Gerstein, M.; Frydman, J. Diverse Cellular Functions of the Hsp90 Molecular Chaperone Uncovered Using Systems Approaches Cell 2007, 131, 121-135 10.1016/j.cell.2007.07.036
-
(2007)
Cell
, vol.131
, pp. 121-135
-
-
McClellan, A.J.1
Xia, Y.2
Deutschbauer, A.M.3
Davis, R.W.4
Gerstein, M.5
Frydman, J.6
-
11
-
-
84934439633
-
Molecular Interaction Network of the Hsp90 Chaperone System
-
Zhao, R.; Houry, W. A. Molecular Interaction Network of the Hsp90 Chaperone System Adv. Exp. Med. Biol. 2007, 594, 27-36 10.1007/978-0-387-39975-1-3
-
(2007)
Adv. Exp. Med. Biol.
, vol.594
, pp. 27-36
-
-
Zhao, R.1
Houry, W.A.2
-
12
-
-
84930205629
-
The Role of HSP70 and its Co-chaperones in Protein Misfolding, Aggregation and Disease
-
Duncan, E. J.; Cheetham, M. E.; Chapple, J. P.; van der Spuy, J. The Role of HSP70 and its Co-chaperones in Protein Misfolding, Aggregation and Disease Subcell. Biochem. 2015, 78, 243-273 10.1007/978-3-319-11731-7-12
-
(2015)
Subcell. Biochem.
, vol.78
, pp. 243-273
-
-
Duncan, E.J.1
Cheetham, M.E.2
Chapple, J.P.3
Van Der Spuy, J.4
-
13
-
-
0033545978
-
Mechanism of Regulation of Hsp70 Chaperones by DnaJ Cochaperones
-
Laufen, T.; Mayer, M. P.; Beisel, C.; Klostermeier, D.; Mogk, A.; Reinstein, J.; Bukau, B. Mechanism of Regulation of Hsp70 Chaperones by DnaJ Cochaperones Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 5452-5457 10.1073/pnas.96.10.5452
-
(1999)
Proc. Natl. Acad. Sci. U. S. A.
, vol.96
, pp. 5452-5457
-
-
Laufen, T.1
Mayer, M.P.2
Beisel, C.3
Klostermeier, D.4
Mogk, A.5
Reinstein, J.6
Bukau, B.7
-
14
-
-
82755187767
-
Heat shock Protein 70 kDa Chaperone/DnaJ Cochaperone Complex Employs an Unusual Dynamic Interface
-
Ahmad, A.; Bhattacharya, A.; McDonald, R. A.; Cordes, M.; Ellington, B.; Bertelsen, E. B.; Zuiderweg, E. R. Heat shock Protein 70 kDa Chaperone/DnaJ Cochaperone Complex Employs an Unusual Dynamic Interface Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 18966-18971 10.1073/pnas.1111220108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 18966-18971
-
-
Ahmad, A.1
Bhattacharya, A.2
McDonald, R.A.3
Cordes, M.4
Ellington, B.5
Bertelsen, E.B.6
Zuiderweg, E.R.7
-
15
-
-
80054740161
-
Nucleotide Exchange Factors for Hsp70 Chaperones
-
Rampelt, H.; Mayer, M. P.; Bukau, B. Nucleotide Exchange Factors for Hsp70 Chaperones Methods Mol. Biol. 2011, 787, 83-91 10.1007/978-1-61779-295-3-7
-
(2011)
Methods Mol. Biol.
, vol.787
, pp. 83-91
-
-
Rampelt, H.1
Mayer, M.P.2
Bukau, B.3
-
16
-
-
84924187480
-
GrpE, Hsp110/Grp170, HspBP1/Sil1 and BAG Domain Proteins: Nucleotide Exchange Factors for Hsp70 Molecular Chaperones
-
Bracher, A.; Verghese, J. GrpE, Hsp110/Grp170, HspBP1/Sil1 and BAG Domain Proteins: Nucleotide Exchange Factors for Hsp70 Molecular Chaperones Subcell. Biochem. 2015, 78, 1-33 10.1007/978-3-319-11731-7-1
-
(2015)
Subcell. Biochem.
, vol.78
, pp. 1-33
-
-
Bracher, A.1
Verghese, J.2
-
17
-
-
0028240468
-
Structural Basis of the 70-kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity. II. Structure of the Active Site with ADP or ATP Bound to Wild Type and Mutant ATPase Fragment
-
Flaherty, K. M.; Wilbanks, S. M.; DeLuca-Flaherty, C.; McKay, D. B. Structural Basis of the 70-kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity. II. Structure of the Active Site with ADP or ATP Bound to Wild Type and Mutant ATPase Fragment J. Biol. Chem. 1994, 269, 12899-12907
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 12899-12907
-
-
Flaherty, K.M.1
Wilbanks, S.M.2
DeLuca-Flaherty, C.3
McKay, D.B.4
-
18
-
-
0029937037
-
Structural Analysis of Substrate Binding by the Molecular Chaperone DnaK
-
Zhu, X. T.; Zhao, X.; Burkholder, W. F.; Gragerov, A.; Ogata, C. M.; Gottesman, M. E.; Hendrickson, W. A. Structural Analysis of Substrate Binding by the Molecular Chaperone DnaK Science 1996, 272, 1606-1614 10.1126/science.272.5268.1606
-
(1996)
Science
, vol.272
, pp. 1606-1614
-
-
Zhu, X.T.1
Zhao, X.2
Burkholder, W.F.3
Gragerov, A.4
Ogata, C.M.5
Gottesman, M.E.6
Hendrickson, W.A.7
-
19
-
-
0030936995
-
Crystal Structure of the Nucleotide Exchange Factor GrpE Bound to the ATPase Domain of the Molecular Chaperone DnaK
-
Harrison, C. J.; Hayer-Hartl, M.; Di Liberto, M.; Hartl, F.; Kuriyan, J. Crystal Structure of the Nucleotide Exchange Factor GrpE Bound to the ATPase Domain of the Molecular Chaperone DnaK Science 1997, 276, 431-435 10.1126/science.276.5311.431
-
(1997)
Science
, vol.276
, pp. 431-435
-
-
Harrison, C.J.1
Hayer-Hartl, M.2
Di Liberto, M.3
Hartl, F.4
Kuriyan, J.5
-
20
-
-
0033136014
-
Structure of a New Crystal Form of Human Hsp70 ATPase Domain
-
Osipiuk, J.; Walsh, M. A.; Freeman, B. C.; Morimoto, R. I.; Joachimiak, A. Structure of a New Crystal Form of Human Hsp70 ATPase Domain Acta Crystallogr., Sect. D: Biol. Crystallogr. 1999, 55, 1105-1107 10.1107/S0907444999002103
-
(1999)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.55
, pp. 1105-1107
-
-
Osipiuk, J.1
Walsh, M.A.2
Freeman, B.C.3
Morimoto, R.I.4
Joachimiak, A.5
-
21
-
-
0029937037
-
Structural Analysis of Substrate Binding by the Molecular Chaperone DnaK
-
Zhu, X. T.; Zhao, X.; Burkholder, W. F.; Gragerov, A.; Ogata, C. M.; Gottesman, M. E.; Hendrickson, W. A. Structural Analysis of Substrate Binding by the Molecular Chaperone DnaK Science 1996, 272, 1606-1614 10.1126/science.272.5268.1606
-
(1996)
Science
, vol.272
, pp. 1606-1614
-
-
Zhu, X.T.1
Zhao, X.2
Burkholder, W.F.3
Gragerov, A.4
Ogata, C.M.5
Gottesman, M.E.6
Hendrickson, W.A.7
-
22
-
-
0142148040
-
The Solution Structure of the Bacterial Hsp70 Chaperone Protein Domain DnaK (393-507) in Complex with the Peptide NRLLLTG
-
Stevens, S. Y.; Cai, S.; Pellecchia, M.; Zuiderweg, E. R. The Solution Structure of the Bacterial Hsp70 Chaperone Protein Domain DnaK (393-507) in Complex with the Peptide NRLLLTG Protein Sci. 2003, 12, 2588-2596 10.1110/ps.03269103
-
(2003)
Protein Sci.
, vol.12
, pp. 2588-2596
-
-
Stevens, S.Y.1
Cai, S.2
Pellecchia, M.3
Zuiderweg, E.R.4
-
23
-
-
0033603631
-
High-Resolution Solution Structure of the 18 kDa Substrate-Binding Domain of the Mammalian Chaperone Protein Hsc70
-
Morshauser, R. C.; Hu, W.; Wang, H.; Pang, Y.; Flynn, G. C.; Zuiderweg, E. R. High-Resolution Solution Structure of the 18 kDa Substrate-Binding Domain of the Mammalian Chaperone Protein Hsc70 J. Mol. Biol. 1999, 289, 1387-1403 10.1006/jmbi.1999.2776
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 1387-1403
-
-
Morshauser, R.C.1
Hu, W.2
Wang, H.3
Pang, Y.4
Flynn, G.C.5
Zuiderweg, E.R.6
-
24
-
-
0034127485
-
Structural Insights into Substrate Binding by the Molecular Chaperone DnaK
-
Pellecchia, M.; Montgomery, D.-L.; Stevens, S.-Y.; Vander Kooi, C.-W.; Feng, H.-P.; Gierasch, L.-M.; Zuiderweg, E.-R. Structural Insights into Substrate Binding by the Molecular Chaperone DnaK Nat. Struct. Biol. 2000, 7, 298-303 10.1038/74062
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 298-303
-
-
Pellecchia, M.1
Montgomery, D.-L.2
Stevens, S.-Y.3
Vander Kooi, C.-W.4
Feng, H.-P.5
Gierasch, L.-M.6
Zuiderweg, E.-R.7
-
25
-
-
33644990203
-
Direct Comparison of a Stable Isolated Hsp70 Substrate-Binding Domain in the Empty and Substrate-Bound States
-
Swain, J. F.; Schulz, E. G.; Gierasch, L. M. Direct Comparison of a Stable Isolated Hsp70 Substrate-Binding Domain in the Empty and Substrate-Bound States J. Biol. Chem. 2006, 281, 1605-1611 10.1074/jbc.M509356200
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 1605-1611
-
-
Swain, J.F.1
Schulz, E.G.2
Gierasch, L.M.3
-
26
-
-
34047268015
-
Hsp70 Chaperone Ligands Control Domain Association via an Allosteric Mechanism Mediated by the Interdomain Linker
-
Swain, J. F.; Dinler, G.; Sivendran, R.; Montgomery, D. L.; Stotz, M.; Gierasch, L. M. Hsp70 Chaperone Ligands Control Domain Association via an Allosteric Mechanism Mediated by the Interdomain Linker Mol. Cell 2007, 26, 27-39 10.1016/j.molcel.2007.02.020
-
(2007)
Mol. Cell
, vol.26
, pp. 27-39
-
-
Swain, J.F.1
Dinler, G.2
Sivendran, R.3
Montgomery, D.L.4
Stotz, M.5
Gierasch, L.M.6
-
27
-
-
33745183353
-
Amide Hydrogen Exchange Reveals Conformational Changes in Hsp70 Chaperones Important for Allosteric Regulation
-
Rist, W.; Graf, C.; Bukau, B.; Mayer, M. P. Amide Hydrogen Exchange Reveals Conformational Changes in Hsp70 Chaperones Important for Allosteric Regulation J. Biol. Chem. 2006, 281, 16493-16501 10.1074/jbc.M600847200
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 16493-16501
-
-
Rist, W.1
Graf, C.2
Bukau, B.3
Mayer, M.P.4
-
28
-
-
84870916379
-
An Interdomain Energetic Tug-of-War Creates the Allosterically Active State in Hsp70 Molecular Chaperones
-
Zhuravleva, A.; Clerico, E. M.; Gierasch, L. M. An Interdomain Energetic Tug-of-War Creates the Allosterically Active State in Hsp70 Molecular Chaperones Cell 2012, 151, 1296-1307 10.1016/j.cell.2012.11.002
-
(2012)
Cell
, vol.151
, pp. 1296-1307
-
-
Zhuravleva, A.1
Clerico, E.M.2
Gierasch, L.M.3
-
29
-
-
0029037015
-
Nucleotide-Induced Conformational Changes in the ATPase and Substrate Binding Domains of the DnaK Chaperone Provide Evidence for Interdomain Communication
-
Buchberger, A.; Theyssen, H.; Schröder, H.; McCarty, J. S.; Virgallita, G.; Milkereit, P.; Reinstein, J.; Bukau, B. Nucleotide-Induced Conformational Changes in the ATPase and Substrate Binding Domains of the DnaK Chaperone Provide Evidence for Interdomain Communication J. Biol. Chem. 1995, 270, 16903-16910 10.1074/jbc.270.28.16903
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 16903-16910
-
-
Buchberger, A.1
Theyssen, H.2
Schröder, H.3
McCarty, J.S.4
Virgallita, G.5
Milkereit, P.6
Reinstein, J.7
Bukau, B.8
-
30
-
-
31344456740
-
The Allosteric Transition in DnaK Probed by Infrared Difference Spectroscopy. Concerted ATP-induced Rearrangement of the Substrate Binding Domain
-
Moro, F.; Fernández-Sáiz, V.; Muga, A. The Allosteric Transition in DnaK Probed by Infrared Difference Spectroscopy. Concerted ATP-induced Rearrangement of the Substrate Binding Domain Protein Sci. 2006, 15, 223-233 10.1110/ps.051732706
-
(2006)
Protein Sci.
, vol.15
, pp. 223-233
-
-
Moro, F.1
Fernández-Sáiz, V.2
Muga, A.3
-
31
-
-
64649094781
-
Solution Conformation of Wild-Type E. Coli Hsp70 (DnaK) Chaperone Complexed with ADP and Substrate
-
Bertelsen, E. B.; Chang, L.; Gestwicki, J. E.; Zuiderweg, E. R. Solution Conformation of Wild-Type E. coli Hsp70 (DnaK) Chaperone Complexed with ADP and Substrate Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 8471-8476 10.1073/pnas.0903503106
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 8471-8476
-
-
Bertelsen, E.B.1
Chang, L.2
Gestwicki, J.E.3
Zuiderweg, E.R.4
-
32
-
-
84871689599
-
Structure and Dynamics of the ATP-bound Open Conformation of Hsp70 Chaperones
-
Kityk, R.; Kopp, J.; Sinning, I.; Mayer, M. P. Structure and Dynamics of the ATP-bound Open Conformation of Hsp70 Chaperones Mol. Cell 2012, 48, 863-874 10.1016/j.molcel.2012.09.023
-
(2012)
Mol. Cell
, vol.48
, pp. 863-874
-
-
Kityk, R.1
Kopp, J.2
Sinning, I.3
Mayer, M.P.4
-
33
-
-
84880167772
-
Allosteric Opening of the Polypeptide-Binding Site When an Hsp70 Binds ATP
-
Qi, R.; Sarbeng, E. B.; Liu, Q.; Le, K. Q.; Xu, X.; Xu, H.; Yang, J.; Wong, J. L.; Vorvis, C.; Hendrickson, W. A.; Zhou, L.; Liu, Q. Allosteric Opening of the Polypeptide-Binding Site When an Hsp70 Binds ATP Nat. Struct. Mol. Biol. 2013, 20, 900-907 10.1038/nsmb.2583
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 900-907
-
-
Qi, R.1
Sarbeng, E.B.2
Liu, Q.3
Le, K.Q.4
Xu, X.5
Xu, H.6
Yang, J.7
Wong, J.L.8
Vorvis, C.9
Hendrickson, W.A.10
Zhou, L.11
Liu, Q.12
-
34
-
-
79952364237
-
Mechanics of Hsp70 Chaperones Enables Differential interaction with Client Proteins
-
Schlecht, R.; Erbse, A. H.; Bukau, B.; Mayer, M. P. Mechanics of Hsp70 Chaperones Enables Differential interaction with Client Proteins Nat. Struct. Mol. Biol. 2011, 18, 345-351 10.1038/nsmb.2006
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 345-351
-
-
Schlecht, R.1
Erbse, A.H.2
Bukau, B.3
Mayer, M.P.4
-
35
-
-
77950431096
-
The Conformational Dynamics of the Mitochondrial Hsp70 Chaperone
-
Mapa, K.; Sikor, M.; Kudryavtsev, V.; Waegemann, K.; Kalinin, S.; Seidel, C. A.; Neupert, W.; Lamb, D. C.; Mokranjac, D. The Conformational Dynamics of the Mitochondrial Hsp70 Chaperone Mol. Cell 2010, 38, 89-100 10.1016/j.molcel.2010.03.010
-
(2010)
Mol. Cell
, vol.38
, pp. 89-100
-
-
Mapa, K.1
Sikor, M.2
Kudryavtsev, V.3
Waegemann, K.4
Kalinin, S.5
Seidel, C.A.6
Neupert, W.7
Lamb, D.C.8
Mokranjac, D.9
-
36
-
-
84878617377
-
Real-Time Observation of the Conformational Dynamics of Mitochondrial Hsp70 by spFRET
-
Sikor, M.; Mapa, K.; von Voithenberg, L. V.; Mokranjac, D.; Lamb, D. C. Real-Time Observation of the Conformational Dynamics of Mitochondrial Hsp70 by spFRET EMBO J. 2013, 32, 1639-1649 10.1038/emboj.2013.89
-
(2013)
EMBO J.
, vol.32
, pp. 1639-1649
-
-
Sikor, M.1
Mapa, K.2
Von Voithenberg, L.V.3
Mokranjac, D.4
Lamb, D.C.5
-
37
-
-
76749141462
-
Energetics of Nucleotide-Induced DnaK Conformational States
-
Taneva, S. G.; Moro, F.; Velázquez-Campoy, A.; Muga, A. Energetics of Nucleotide-Induced DnaK Conformational States Biochemistry 2010, 49, 1338-1345 10.1021/bi901847q
-
(2010)
Biochemistry
, vol.49
, pp. 1338-1345
-
-
Taneva, S.G.1
Moro, F.2
Velázquez-Campoy, A.3
Muga, A.4
-
38
-
-
84930939681
-
Substrate-Binding Domain Conformational Dynamics Mediate Hsp70 Allostery
-
Zhuravleva, A.; Gierasch, L. M. Substrate-Binding Domain Conformational Dynamics Mediate Hsp70 Allostery Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E2865-E2873 10.1073/pnas.1506692112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. E2865-E2873
-
-
Zhuravleva, A.1
Gierasch, L.M.2
-
39
-
-
0032417764
-
Mutations in the DnaK Chaperone Affecting Interaction with the DnaJ Cochaperone
-
Gassler, C. S.; Buchberger, A.; Laufen, T.; Mayer, M. P.; Schroder, H.; Valencia, A.; Bukau, B. Mutations in the DnaK Chaperone Affecting Interaction with the DnaJ Cochaperone Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 15229-15234 10.1073/pnas.95.26.15229
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 15229-15234
-
-
Gassler, C.S.1
Buchberger, A.2
Laufen, T.3
Mayer, M.P.4
Schroder, H.5
Valencia, A.6
Bukau, B.7
-
40
-
-
0029778854
-
Mutations in the C-terminal Fragment of DnaK Affecting Peptide Binding
-
Burkholder, W. F.; Zhao, X.; Zhu, X.; Hendrickson, W. A.; Gragerov, A.; Gottesman, M. E. Mutations in the C-terminal Fragment of DnaK Affecting Peptide Binding Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 10632-10637 10.1073/pnas.93.20.10632
-
(1996)
Proc. Natl. Acad. Sci. U. S. A.
, vol.93
, pp. 10632-10637
-
-
Burkholder, W.F.1
Zhao, X.2
Zhu, X.3
Hendrickson, W.A.4
Gragerov, A.5
Gottesman, M.E.6
-
41
-
-
0033605086
-
Mutations in the Substrate Binding Domain of the Escherichia coli 70 kDa Molecular Chaperone, DnaK, Which Alter Substrate Affinity or Interdomain Coupling
-
Montgomery, D. L.; Morimoto, R. I.; Gierasch, L. M. Mutations in the Substrate Binding Domain of the Escherichia coli 70 kDa Molecular Chaperone, DnaK, Which Alter Substrate Affinity or Interdomain Coupling J. Mol. Biol. 1999, 286, 915-932 10.1006/jmbi.1998.2514
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 915-932
-
-
Montgomery, D.L.1
Morimoto, R.I.2
Gierasch, L.M.3
-
42
-
-
31544442176
-
Allosteric Regulation of Hsp70 Chaperones by a Proline Switch
-
Vogel, M.; Bukau, B.; Mayer, M. P. Allosteric Regulation of Hsp70 Chaperones by a Proline Switch Mol. Cell 2006, 21, 359-367 10.1016/j.molcel.2005.12.017
-
(2006)
Mol. Cell
, vol.21
, pp. 359-367
-
-
Vogel, M.1
Bukau, B.2
Mayer, M.P.3
-
43
-
-
33846020582
-
Allosteric Regulation of Hsp70 Chaperones Involves a Conserved Interdomain Linker
-
Vogel, M.; Mayer, M. P.; Bukau, B. Allosteric Regulation of Hsp70 Chaperones Involves a Conserved Interdomain Linker J. Biol. Chem. 2006, 281, 38705-38711 10.1074/jbc.M609020200
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 38705-38711
-
-
Vogel, M.1
Mayer, M.P.2
Bukau, B.3
-
44
-
-
77957274298
-
An interdomain sector mediating allostery in Hsp70 molecular chaperones
-
Smock, R. G.; Rivoire, O.; Russ, W. P.; Swain, J. F.; Leibler, S.; Ranganathan, R.; Gierasch, L. M. An interdomain sector mediating allostery in Hsp70 molecular chaperones Mol. Syst. Biol. 2010, 6, 414 10.1038/msb.2010.65
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 414
-
-
Smock, R.G.1
Rivoire, O.2
Russ, W.P.3
Swain, J.F.4
Leibler, S.5
Ranganathan, R.6
Gierasch, L.M.7
-
45
-
-
0033936317
-
Multistep Mechanism of Substrate Binding Determines Chaperone Activity of Hsp70
-
Mayer, M. P.; Schroder, H.; Rudiger, S.; Paal, K.; Laufen, T.; Bukau, B. Multistep Mechanism of Substrate Binding Determines Chaperone Activity of Hsp70 Nat. Struct. Biol. 2000, 7, 586-593 10.1038/76819
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 586-593
-
-
Mayer, M.P.1
Schroder, H.2
Rudiger, S.3
Paal, K.4
Laufen, T.5
Bukau, B.6
-
46
-
-
0033783190
-
Molecular Basis for Interactions of the DnaK Chaperone with Substrates
-
Mayer, M. P.; Rudiger, S.; Bukau, B. Molecular Basis for Interactions of the DnaK Chaperone with Substrates Biol. Chem. 2000, 381, 877-885 10.1515/BC.2000.109
-
(2000)
Biol. Chem.
, vol.381
, pp. 877-885
-
-
Mayer, M.P.1
Rudiger, S.2
Bukau, B.3
-
47
-
-
2442444156
-
The Lid Subdomain of DnaK is Required for the Stabilization of the Substrate-Binding Site
-
Moro, F.; Fernandez-Saiz, V.; Muga, A. The Lid Subdomain of DnaK is Required for the Stabilization of the Substrate-Binding Site J. Biol. Chem. 2004, 279, 19600-19606 10.1074/jbc.M400921200
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 19600-19606
-
-
Moro, F.1
Fernandez-Saiz, V.2
Muga, A.3
-
48
-
-
0037413822
-
Interdomain Interaction Through Helices A and B of DnaK Peptide Binding Domain
-
Moro, F.; Fernandez, V.; Muga, A. Interdomain Interaction Through Helices A and B of DnaK Peptide Binding Domain FEBS Lett. 2003, 533, 119-123 10.1016/S0014-5793(02)03752-3
-
(2003)
FEBS Lett.
, vol.533
, pp. 119-123
-
-
Moro, F.1
Fernandez, V.2
Muga, A.3
-
49
-
-
0037952785
-
Importance of the D and e Helices of the Molecular Chaperone DnaK for ATP Binding and Substrate Release
-
Slepenkov, S. V.; Patchen, B.; Peterson, K. M.; Witt, S. N. Importance of the D and E Helices of the Molecular Chaperone DnaK for ATP Binding and Substrate Release Biochemistry 2003, 42, 5867-5876 10.1021/bi034126v
-
(2003)
Biochemistry
, vol.42
, pp. 5867-5876
-
-
Slepenkov, S.V.1
Patchen, B.2
Peterson, K.M.3
Witt, S.N.4
-
50
-
-
84942019140
-
Pathways of Allosteric Regulation in Hsp70 Chaperones
-
Kityk, R.; Vogel, M.; Schlecht, R.; Bukau, B.; Mayer, M. P. Pathways of Allosteric Regulation in Hsp70 Chaperones Nat. Commun. 2015, 6, 8308 10.1038/ncomms9308
-
(2015)
Nat. Commun.
, vol.6
, pp. 8308
-
-
Kityk, R.1
Vogel, M.2
Schlecht, R.3
Bukau, B.4
Mayer, M.P.5
-
51
-
-
84904810553
-
Crystal Structure of the Stress-Inducible Human Heat Shock Protein 70 Substrate-Binding Domain in Complex with Peptide Substrate
-
Zhang, P.; Leu, J. I.; Murphy, M. E.; George, D. L.; Marmorstein, R. Crystal Structure of the Stress-Inducible Human Heat Shock Protein 70 Substrate-Binding Domain in Complex With Peptide Substrate PLoS One 2014, 9, e103518 10.1371/journal.pone.0103518
-
(2014)
PLoS One
, vol.9
, pp. e103518
-
-
Zhang, P.1
Leu, J.I.2
Murphy, M.E.3
George, D.L.4
Marmorstein, R.5
-
52
-
-
33746330168
-
Hsp70 Molecular Chaperones: Emerging Roles in Human Disease and Identification of Small Molecule Modulators
-
Brodsky, J. L.; Chiosis, G. Hsp70 Molecular Chaperones: Emerging Roles in Human Disease and Identification of Small Molecule Modulators Curr. Top. Med. Chem. 2006, 6, 1215-1225 10.2174/156802606777811997
-
(2006)
Curr. Top. Med. Chem.
, vol.6
, pp. 1215-1225
-
-
Brodsky, J.L.1
Chiosis, G.2
-
53
-
-
74249097474
-
Pharmacological Targeting of the Hsp70 Chaperone
-
Patury, S.; Miyata, Y.; Gestwicki, J.-E. Pharmacological Targeting of the Hsp70 Chaperone Curr. Top. Med. Chem. 2009, 9, 1337-1351 10.2174/156802609789895674
-
(2009)
Curr. Top. Med. Chem.
, vol.9
, pp. 1337-1351
-
-
Patury, S.1
Miyata, Y.2
Gestwicki, J.-E.3
-
54
-
-
70349292883
-
Small molecule DnaK modulators targeting the betadomain
-
Cellitti, J.; Zhang, Z.; Wang, S.; Wu, B.; Yuan, H.; Hasegawa, P.; Guiney, D. G.; Pellecchia, M. Small molecule DnaK modulators targeting the betadomain Chem. Biol. Drug Des. 2009, 74, 349-357 10.1111/j.1747-0285.2009.00869.x
-
(2009)
Chem. Biol. Drug Des.
, vol.74
, pp. 349-357
-
-
Cellitti, J.1
Zhang, Z.2
Wang, S.3
Wu, B.4
Yuan, H.5
Hasegawa, P.6
Guiney, D.G.7
Pellecchia, M.8
-
55
-
-
78751478982
-
Peptides and Aptamers Targeting Hsp70: A Novel Approach for Anticancer Chemotherapy
-
Rérole, A.-L.; Gobbo, J.; De Thonel, A.; Schmitt, E.; Pais de Barros, J.-P.; Hammann, A.; Lanneau, D.; Fourmaux, E.; Deminov, O. N.; Micheau, O.; Lagrost, L.; Colas, P.; Kroemer, G.; Garrido, C. Peptides and Aptamers Targeting Hsp70: A Novel Approach for Anticancer Chemotherapy Cancer Res. 2011, 71, 484-495 10.1158/0008-5472.CAN-10-1443
-
(2011)
Cancer Res.
, vol.71
, pp. 484-495
-
-
Rérole, A.-L.1
Gobbo, J.2
De Thonel, A.3
Schmitt, E.4
Pais De Barros, J.-P.5
Hammann, A.6
Lanneau, D.7
Fourmaux, E.8
Deminov, O.N.9
Micheau, O.10
Lagrost, L.11
Colas, P.12
Kroemer, G.13
Garrido, C.14
-
56
-
-
77953734857
-
Heat Shock Protein 70 (Hsp70) as an Emerging Drug Target
-
Evans, C. G.; Chang, L.; Gestwicki, J. E. Heat Shock Protein 70 (Hsp70) as an Emerging Drug Target J. Med. Chem. 2010, 53, 4585-4602 10.1021/jm100054f
-
(2010)
J. Med. Chem.
, vol.53
, pp. 4585-4602
-
-
Evans, C.G.1
Chang, L.2
Gestwicki, J.E.3
-
57
-
-
84904440151
-
Heat Shock Protein 70 - The Next Chaperone to Target in the Treatment of Human Acute Myelogenous Leukemia?
-
Reikvam, H.; Brenner, A. K.; Nepstad, I.; Sulen, A.; Bruserud, Ø. Heat Shock Protein 70-The Next Chaperone to Target in the Treatment of Human Acute Myelogenous Leukemia? Expert Opin. Ther. Targets 2014, 18, 929-944 10.1517/14728222.2014.924925
-
(2014)
Expert Opin. Ther. Targets
, vol.18
, pp. 929-944
-
-
Reikvam, H.1
Brenner, A.K.2
Nepstad, I.3
Sulen, A.4
Bruserud, Ø.5
-
58
-
-
84876728531
-
Hsp70 Protein Complexes as Drug Targets
-
Assimon, V. A.; Gillies, A. T.; Rauch, J. N.; Gestwicki, J. E. Hsp70 Protein Complexes as Drug Targets Curr. Pharm. Des. 2013, 19, 404-417 10.2174/138161213804143699
-
(2013)
Curr. Pharm. Des.
, vol.19
, pp. 404-417
-
-
Assimon, V.A.1
Gillies, A.T.2
Rauch, J.N.3
Gestwicki, J.E.4
-
59
-
-
0035847010
-
Identification of an Inhibitor of Hsc70-Mediated Protein Translocation and ATP Hydrolysis
-
Fewell, S. W.; Day, B. W.; Brodsky, J. L. Identification of an Inhibitor of Hsc70-Mediated Protein Translocation and ATP Hydrolysis J. Biol. Chem. 2001, 276, 910-914 10.1074/jbc.M008535200
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 910-914
-
-
Fewell, S.W.1
Day, B.W.2
Brodsky, J.L.3
-
60
-
-
10944263745
-
Small Molecule Modulators of Endogenous and Co-chaperone Stimulated Hsp70 ATPase Activity
-
Fewell, S. W.; Smith, C. M.; Lyon, M. A.; Dumitrescu, T. P.; Wipf, P.; Day, B. W.; Brodsky, J. L. Small Molecule Modulators of Endogenous and Co-chaperone Stimulated Hsp70 ATPase Activity J. Biol. Chem. 2004, 279, 51131-51140 10.1074/jbc.M404857200
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 51131-51140
-
-
Fewell, S.W.1
Smith, C.M.2
Lyon, M.A.3
Dumitrescu, T.P.4
Wipf, P.5
Day, B.W.6
Brodsky, J.L.7
-
61
-
-
36148989163
-
High-Throughput Screen for Small Molecules that Modulate the ATPase Activity of the Molecular Chaperone DnaK
-
Chang, L.; Bertelsen, E. B.; Wisén, S.; Larsen, E. M.; Zuiderweg, E. R.; Gestwicki, J. E. High-Throughput Screen for Small Molecules that Modulate the ATPase Activity of the Molecular Chaperone DnaK Anal. Biochem. 2008, 372, 167-176 10.1016/j.ab.2007.08.020
-
(2008)
Anal. Biochem.
, vol.372
, pp. 167-176
-
-
Chang, L.1
Bertelsen, E.B.2
Wisén, S.3
Larsen, E.M.4
Zuiderweg, E.R.5
Gestwicki, J.E.6
-
62
-
-
39149117364
-
Identification of Small Molecules that Modify the Protein Folding Activity of Heat Shock Protein 70
-
Wisén, S.; Gestwicki, J. E. Identification of Small Molecules that Modify the Protein Folding Activity of Heat Shock Protein 70 Anal. Biochem. 2008, 374, 371-377 10.1016/j.ab.2007.12.009
-
(2008)
Anal. Biochem.
, vol.374
, pp. 371-377
-
-
Wisén, S.1
Gestwicki, J.E.2
-
63
-
-
64349121987
-
Novel Adenosine-Derived Inhibitors of 70 kDa Heat Shock Protein, Discovered Through Structure-Based Design
-
Williamson, D. S.; Borgognoni, J.; Clay, A.; Daniels, Z.; Dokurno, P.; Drysdale, M. J.; Foloppe, N.; Francis, G. L.; Graham, C. J.; Howes, R.; Macias, A. T.; Murray, J. B.; Parsons, R.; Shaw, T.; Surgenor, A. E.; Terry, L.; Wang, Y.; Wood, M.; Massey, A. J. Novel Adenosine-Derived Inhibitors of 70 kDa Heat Shock Protein, Discovered Through Structure-Based Design J. Med. Chem. 2009, 52, 1510-1513 10.1021/jm801627a
-
(2009)
J. Med. Chem.
, vol.52
, pp. 1510-1513
-
-
Williamson, D.S.1
Borgognoni, J.2
Clay, A.3
Daniels, Z.4
Dokurno, P.5
Drysdale, M.J.6
Foloppe, N.7
Francis, G.L.8
Graham, C.J.9
Howes, R.10
Macias, A.T.11
Murray, J.B.12
Parsons, R.13
Shaw, T.14
Surgenor, A.E.15
Terry, L.16
Wang, Y.17
Wood, M.18
Massey, A.J.19
-
64
-
-
77954662908
-
A Novel, Small Molecule Inhibitor of Hsc70/Hsp70 Potentiates Hsp90 Inhibitor Induced Apoptosis in HCT116 Colon Carcinoma Cells
-
Massey, A. J.; Williamson, D. S.; Browne, H.; Murray, J. B.; Dokurno, P.; Shaw, T.; Macias, A. T.; Daniels, Z.; Geoffroy, S.; Dopson, M.; Lavan, P.; Matassova, N.; Francis, G. L.; Graham, C. J.; Parsons, R.; Wang, Y.; Padfield, A.; Comer, M.; Drysdale, M. J.; Wood, M. A Novel, Small Molecule Inhibitor of Hsc70/Hsp70 Potentiates Hsp90 Inhibitor Induced Apoptosis in HCT116 Colon Carcinoma Cells Cancer Chemother. Pharmacol. 2010, 66, 535-545 10.1007/s00280-009-1194-3
-
(2010)
Cancer Chemother. Pharmacol.
, vol.66
, pp. 535-545
-
-
Massey, A.J.1
Williamson, D.S.2
Browne, H.3
Murray, J.B.4
Dokurno, P.5
Shaw, T.6
Macias, A.T.7
Daniels, Z.8
Geoffroy, S.9
Dopson, M.10
Lavan, P.11
Matassova, N.12
Francis, G.L.13
Graham, C.J.14
Parsons, R.15
Wang, Y.16
Padfield, A.17
Comer, M.18
Drysdale, M.J.19
Wood, M.20
more..
-
65
-
-
84893203556
-
Functional Analysis of Hsp70 Inhibitors
-
Schlecht, R.; Scholz, S. R.; Dahmen, H.; Wegener, A.; Sirrenberg, C.; Musil, D.; Bomke, J.; Eggenweiler, H. M.; Mayer, M. P.; Bukau, B. Functional Analysis of Hsp70 Inhibitors PLoS One 2013, 8, e78443 10.1371/journal.pone.0078443
-
(2013)
PLoS One
, vol.8
, pp. e78443
-
-
Schlecht, R.1
Scholz, S.R.2
Dahmen, H.3
Wegener, A.4
Sirrenberg, C.5
Musil, D.6
Bomke, J.7
Eggenweiler, H.M.8
Mayer, M.P.9
Bukau, B.10
-
66
-
-
70349768075
-
A Small Molecule Inhibitor of Inducible Heat Shock Protein 70
-
Leu, J.-I.; Pimkina, J.; Frank, A.; Murphy, M.-E.; George, D.-L. A Small Molecule Inhibitor of Inducible Heat Shock Protein 70 Mol. Cell 2009, 36, 15-27 10.1016/j.molcel.2009.09.023
-
(2009)
Mol. Cell
, vol.36
, pp. 15-27
-
-
Leu, J.-I.1
Pimkina, J.2
Frank, A.3
Murphy, M.-E.4
George, D.-L.5
-
67
-
-
79960694363
-
Hsp70 Inhibition by the Small Molecule 2-Phenylethynesulfonamide Impairs Protein Clearance Pathways in Tumor Cells
-
Leu, J.-I.; Pimkina, J.; Pandey, P.; Murphy, M.-E.; George, D.-L. Hsp70 Inhibition by the Small Molecule 2-Phenylethynesulfonamide Impairs Protein Clearance Pathways in Tumor Cells Mol. Cancer Res. 2011, 9, 936-947 10.1158/1541-7786.MCR-11-0019
-
(2011)
Mol. Cancer Res.
, vol.9
, pp. 936-947
-
-
Leu, J.-I.1
Pimkina, J.2
Pandey, P.3
Murphy, M.-E.4
George, D.-L.5
-
68
-
-
84890860170
-
Identification of an Allosteric Pocket on Human Hsp70 Reveals a Mode of Inhibition of This Therapeutically Important Protein
-
Rodina, A.; Patel, P. D.; Kang, Y.; Patel, Y.; Baaklini, I.; Wong, M. J.; Taldone, T.; Yan, P.; Yang, C.; Maharaj, R.; Gozman, A.; Patel, M. R.; Patel, H. J.; Chirico, W.; Erdjument-Bromage, H.; Talele, T. T.; Young, J. C.; Chiosis, G. Identification of an Allosteric Pocket on Human Hsp70 Reveals a Mode of Inhibition of This Therapeutically Important Protein Chem. Biol. 2013, 20, 1469-1480 10.1016/j.chembiol.2013.10.008
-
(2013)
Chem. Biol.
, vol.20
, pp. 1469-1480
-
-
Rodina, A.1
Patel, P.D.2
Kang, Y.3
Patel, Y.4
Baaklini, I.5
Wong, M.J.6
Taldone, T.7
Yan, P.8
Yang, C.9
Maharaj, R.10
Gozman, A.11
Patel, M.R.12
Patel, H.J.13
Chirico, W.14
Erdjument-Bromage, H.15
Talele, T.T.16
Young, J.C.17
Chiosis, G.18
-
69
-
-
84896860139
-
Heat Shock Protein 70 Inhibitors. 1. 2,5′-Thiodipyrimidine and 5-(Phenylthio)Pyrimidine Acrylamides as Irreversible Binders to an Allosteric Site on Heat Shock Protein 70
-
Kang, Y.; Taldone, T.; Patel, H. J.; Patel, P. D.; Rodina, A.; Gozman, A.; Maharaj, R.; Clement, C. C.; Patel, M. R.; Brodsky, J. L.; Young, J. C.; Chiosis, G. Heat Shock Protein 70 Inhibitors. 1. 2,5′-Thiodipyrimidine and 5-(Phenylthio)Pyrimidine Acrylamides as Irreversible Binders to an Allosteric Site on Heat Shock Protein 70 J. Med. Chem. 2014, 57, 1188-1207 10.1021/jm401551n
-
(2014)
J. Med. Chem.
, vol.57
, pp. 1188-1207
-
-
Kang, Y.1
Taldone, T.2
Patel, H.J.3
Patel, P.D.4
Rodina, A.5
Gozman, A.6
Maharaj, R.7
Clement, C.C.8
Patel, M.R.9
Brodsky, J.L.10
Young, J.C.11
Chiosis, G.12
-
70
-
-
84896815426
-
Heat Shock Protein 70 Inhibitors. 2. 2,5′-Thiodipyrimidines, 5-(Phenylthio)Pyrimidines, 2-(Pyridin-3ylthio)Pyrimidines, and 3-(Phenylthio)Pyridines as Reversible Binders to an Allosteric Site on Heat Shock Protein 70
-
Taldone, T.; Kang, Y.; Patel, H. J.; Patel, M. R.; Patel, P. D.; Rodina, A.; Patel, Y.; Gozman, A.; Maharaj, R.; Clement, C. C.; Lu, A.; Young, J. C.; Chiosis, G. Heat Shock Protein 70 Inhibitors. 2. 2,5′-Thiodipyrimidines, 5-(Phenylthio)Pyrimidines, 2-(Pyridin-3ylthio)Pyrimidines, and 3-(Phenylthio)Pyridines as Reversible Binders to an Allosteric Site on Heat Shock Protein 70 J. Med. Chem. 2014, 57, 1208-1224 10.1021/jm401552y
-
(2014)
J. Med. Chem.
, vol.57
, pp. 1208-1224
-
-
Taldone, T.1
Kang, Y.2
Patel, H.J.3
Patel, M.R.4
Patel, P.D.5
Rodina, A.6
Patel, Y.7
Gozman, A.8
Maharaj, R.9
Clement, C.C.10
Lu, A.11
Young, J.C.12
Chiosis, G.13
-
71
-
-
84914104764
-
Structural Basis for the Inhibition of Hsp70 and DnaK Chaperones by Small-Molecule Targeting of a C-terminal Allosteric Pocket
-
Leu, J. I.; Zhang, P.; Murphy, M. E.; Marmorstein, R.; George, D. L. Structural Basis for the Inhibition of Hsp70 and DnaK Chaperones by Small-Molecule Targeting of a C-terminal Allosteric Pocket ACS Chem. Biol. 2014, 9, 2508-2516 10.1021/cb500236y
-
(2014)
ACS Chem. Biol.
, vol.9
, pp. 2508-2516
-
-
Leu, J.I.1
Zhang, P.2
Murphy, M.E.3
Marmorstein, R.4
George, D.L.5
-
72
-
-
84941807135
-
Efficacy of the Hsp70 Inhibitor PET-16 in Multiple Myeloma
-
Bailey, C. K.; Budina-Kolomets, A.; Murphy, M. E.; Nefedova, Y. Efficacy of the Hsp70 Inhibitor PET-16 in Multiple Myeloma Cancer Biol. Ther. 2015, 16, 1422-1426 10.1080/15384047.2015.1071743
-
(2015)
Cancer Biol. Ther.
, vol.16
, pp. 1422-1426
-
-
Bailey, C.K.1
Budina-Kolomets, A.2
Murphy, M.E.3
Nefedova, Y.4
-
73
-
-
84921494281
-
The Novolactone Natural Product Disrupts the Allosteric Regulation of Hsp70
-
Hassan, A. Q.; Kirby, C. A.; Zhou, W.; Schuhmann, T.; Kityk, R.; Kipp, D. R.; Baird, J.; Chen, J.; Chen, Y.; Chung, F.; Hoepfner, D.; Movva, N. R.; Pagliarini, R.; Petersen, F.; Quinn, C.; Quinn, D.; Riedl, R.; Schmitt, E. K.; Schitter, A.; Stams, T.; Studer, C.; Fortin, P. D.; Mayer, M. P.; Sadlish, H. The Novolactone Natural Product Disrupts the Allosteric Regulation of Hsp70 Chem. Biol. 2015, 22, 87-97 10.1016/j.chembiol.2014.11.007
-
(2015)
Chem. Biol.
, vol.22
, pp. 87-97
-
-
Hassan, A.Q.1
Kirby, C.A.2
Zhou, W.3
Schuhmann, T.4
Kityk, R.5
Kipp, D.R.6
Baird, J.7
Chen, J.8
Chen, Y.9
Chung, F.10
Hoepfner, D.11
Movva, N.R.12
Pagliarini, R.13
Petersen, F.14
Quinn, C.15
Quinn, D.16
Riedl, R.17
Schmitt, E.K.18
Schitter, A.19
Stams, T.20
Studer, C.21
Fortin, P.D.22
Mayer, M.P.23
Sadlish, H.24
more..
-
74
-
-
84884603669
-
Inhibitors of Difficult Protein-Protein Interactions Identified by High-Throughput Screening of Multiprotein Complexes
-
Cesa, L. C.; Patury, S.; Komiyama, T.; Ahmad, A.; Zuiderweg, E. R.; Gestwicki, J. E. Inhibitors of Difficult Protein-Protein Interactions Identified by High-Throughput Screening of Multiprotein Complexes ACS Chem. Biol. 2013, 8, 1988-1997 10.1021/cb400356m
-
(2013)
ACS Chem. Biol.
, vol.8
, pp. 1988-1997
-
-
Cesa, L.C.1
Patury, S.2
Komiyama, T.3
Ahmad, A.4
Zuiderweg, E.R.5
Gestwicki, J.E.6
-
75
-
-
78049433050
-
Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs
-
Liu, Y.; Gierasch, L. M.; Bahar, I. Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs PLoS Comput. Biol. 2010, 6, e1000931 10.1371/journal.pcbi.1000931
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000931
-
-
Liu, Y.1
Gierasch, L.M.2
Bahar, I.3
-
76
-
-
84872012970
-
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
-
Chiappori, F.; Merelli, I.; Colombo, G.; Milanesi, L.; Morra, G. Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations PLoS Comput. Biol. 2012, 8, e1002844 10.1371/journal.pcbi.1002844
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002844
-
-
Chiappori, F.1
Merelli, I.2
Colombo, G.3
Milanesi, L.4
Morra, G.5
-
77
-
-
84892702922
-
Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding Through Free Energy Landscape Analysis: ATP Binding to Hsp70
-
Nicolaï, A.; Delarue, P.; Senet, P. Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding Through Free Energy Landscape Analysis: ATP Binding to Hsp70 PLoS Comput. Biol. 2013, 9, e1003379 10.1371/journal.pcbi.1003379
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003379
-
-
Nicolaï, A.1
Delarue, P.2
Senet, P.3
-
78
-
-
84888245316
-
Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. Coli Hsp70/DnaK
-
Ung, P. M.; Thompson, A. D.; Chang, L.; Gestwicki, J. E.; Carlson, H. A. Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK PLoS Comput. Biol. 2013, 9, e1003279 10.1371/journal.pcbi.1003279
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003279
-
-
Ung, P.M.1
Thompson, A.D.2
Chang, L.3
Gestwicki, J.E.4
Carlson, H.A.5
-
79
-
-
84873490543
-
Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation
-
Xu, L.; Hasin, N.; Shen, M.; He, J.; Xue, Y.; Zhou, X.; Perrett, S.; Song, Y.; Jones, G. W. Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation PLoS Comput. Biol. 2013, 9, e1002896 10.1371/journal.pcbi.1002896
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002896
-
-
Xu, L.1
Hasin, N.2
Shen, M.3
He, J.4
Xue, Y.5
Zhou, X.6
Perrett, S.7
Song, Y.8
Jones, G.W.9
-
80
-
-
84901650125
-
ATPase Subdomain IA is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones
-
General, I. J.; Liu, Y.; Blackburn, M. E.; Mao, W.; Gierasch, L. M.; Bahar, I. ATPase Subdomain IA is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones PLoS Comput. Biol. 2014, 10, e1003624 10.1371/journal.pcbi.1003624
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003624
-
-
General, I.J.1
Liu, Y.2
Blackburn, M.E.3
Mao, W.4
Gierasch, L.M.5
Bahar, I.6
-
81
-
-
84957539705
-
Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins
-
Stetz, G.; Verkhivker, G. M. Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins PLoS One 2015, 10, e0143752 10.1371/journal.pone.0143752
-
(2015)
PLoS One
, vol.10
, pp. e0143752
-
-
Stetz, G.1
Verkhivker, G.M.2
-
82
-
-
84951908781
-
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones
-
Malinverni, D.; Marsili, S.; Barducci, A.; De Los Rios, P. Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones PLoS Comput. Biol. 2015, 11, e1004262 10.1371/journal.pcbi.1004262
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004262
-
-
Malinverni, D.1
Marsili, S.2
Barducci, A.3
De Los Rios, P.4
-
83
-
-
84944463599
-
In silico Mutational Studies of Hsp70 Disclose Sites with Distinct Functional Attributes
-
Ozbaykal, G.; Rana Atilgan, A.; Atilgan, C. In silico Mutational Studies of Hsp70 Disclose Sites with Distinct Functional Attributes Proteins: Struct., Funct., Genet. 2015, 83, 2077-2090 10.1002/prot.24925
-
(2015)
Proteins: Struct., Funct., Genet.
, vol.83
, pp. 2077-2090
-
-
Ozbaykal, G.1
Rana Atilgan, A.2
Atilgan, C.3
-
84
-
-
28444453011
-
A Network Representation of Protein Structures: Implications for Protein Stability
-
Brinda, K. V.; Vishveshwara, S. A Network Representation of Protein Structures: Implications for Protein Stability Biophys. J. 2005, 89, 4159-4170 10.1529/biophysj.105.064485
-
(2005)
Biophys. J.
, vol.89
, pp. 4159-4170
-
-
Brinda, K.V.1
Vishveshwara, S.2
-
85
-
-
78649883885
-
Interaction Energy Based Protein Structure Networks
-
Vijayabaskar, M. S.; Vishveshwara, S. Interaction Energy Based Protein Structure Networks Biophys. J. 2010, 99, 3704-3715 10.1016/j.bpj.2010.08.079
-
(2010)
Biophys. J.
, vol.99
, pp. 3704-3715
-
-
Vijayabaskar, M.S.1
Vishveshwara, S.2
-
86
-
-
0346057951
-
Small-World Communication of Residues and Significance for Protein Dynamics
-
Atilgan, A. R.; Akan, P.; Baysal, C. Small-World Communication of Residues and Significance for Protein Dynamics Biophys. J. 2004, 86, 85-91 10.1016/S0006-3495(04)74086-2
-
(2004)
Biophys. J.
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
87
-
-
17444396776
-
Topology of Small-World Networks of Protein-Protein Complex Structures
-
del Sol, A.; Fujihashi, H.; O'Meara, P. Topology of Small-World Networks of Protein-Protein Complex Structures Bioinformatics 2005, 21, 1311-1315 10.1093/bioinformatics/bti167
-
(2005)
Bioinformatics
, vol.21
, pp. 1311-1315
-
-
Del Sol, A.1
Fujihashi, H.2
O'Meara, P.3
-
88
-
-
33748207211
-
Residue Centrality, Functionally Important Residues, and Active Site Shape: Analysis of Enzyme and Non-Enzyme Families
-
del Sol, A.; Fujihashi, H.; Amoros, D.; Nussinov, R. Residue Centrality, Functionally Important Residues, and Active Site Shape: Analysis of Enzyme and Non-Enzyme Families Protein Sci. 2006, 15, 2120-8 10.1110/ps.062249106
-
(2006)
Protein Sci.
, vol.15
, pp. 2120-2128
-
-
Del Sol, A.1
Fujihashi, H.2
Amoros, D.3
Nussinov, R.4
-
89
-
-
8544221118
-
Network Analysis of Protein Structures Identifies Functional Residues
-
Amitai, G.; Shemesh, A.; Sitbon, E.; Shklar, M.; Netanely, D.; Venger, I.; Pietrokovski, S. Network Analysis of Protein Structures Identifies Functional Residues J. Mol. Biol. 2004, 344, 1135-1146 10.1016/j.jmb.2004.10.055
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
Pietrokovski, S.7
-
90
-
-
34347326305
-
Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR
-
Hu, Z.; Bowen, D.; Southerland, W. M.; del Sol, A.; Pan, Y.; Nussinov, R.; Ma, B. Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR PLoS Comput. Biol. 2007, 3, e117 10.1371/journal.pcbi.0030117
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. e117
-
-
Hu, Z.1
Bowen, D.2
Southerland, W.M.3
Del Sol, A.4
Pan, Y.5
Nussinov, R.6
Ma, B.7
-
91
-
-
33745461893
-
Residues Crucial for Maintaining Short Paths in Network Communication Mediate Signaling in Proteins
-
2006.0019
-
del Sol, A.; Fujihashi, H.; Amoros, D.; Nussinov, R. Residues Crucial for Maintaining Short Paths in Network Communication Mediate Signaling in Proteins. Mol. Syst. Biol. 2006, 2, 2006.0019. 10.1038/msb4100063
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Del Sol, A.1
Fujihashi, H.2
Amoros, D.3
Nussinov, R.4
-
92
-
-
84879552995
-
Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK
-
Zahn, M.; Berthold, N.; Kieslich, B.; Knappe, D.; Hoffmann, R.; Sträter, N. Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK J. Mol. Biol. 2013, 425, 2463-2479 10.1016/j.jmb.2013.03.041
-
(2013)
J. Mol. Biol.
, vol.425
, pp. 2463-2479
-
-
Zahn, M.1
Berthold, N.2
Kieslich, B.3
Knappe, D.4
Hoffmann, R.5
Sträter, N.6
-
93
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242 10.1093/nar/28.1.235
-
(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
-
94
-
-
0030442990
-
Positioning Hydrogen Atoms by Optimizing Hydrogen-bond Networks in Protein Structures
-
Hooft, R. W.; Sander, C.; Vriend, G. Positioning Hydrogen Atoms by Optimizing Hydrogen-bond Networks in Protein Structures Proteins: Struct., Funct., Genet. 1996, 26, 363-376 10.1002/(SICI)1097-0134(199612)26:4<363::AID-PROT1>3.0.CO;2-D
-
(1996)
Proteins: Struct., Funct., Genet.
, vol.26
, pp. 363-376
-
-
Hooft, R.W.1
Sander, C.2
Vriend, G.3
-
95
-
-
77954273221
-
WIWS: A Protein Structure Bioinformatics web Service Collection
-
Hekkelman, M. L.; Te Beek, T. A.; Pettifer, S. R.; Thorne, D.; Attwood, T. K.; Vriend, G. WIWS: A Protein Structure Bioinformatics web Service Collection Nucleic Acids Res. 2010, 38, W719-W723 10.1093/nar/gkq453
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W719-W723
-
-
Hekkelman, M.L.1
Te Beek, T.A.2
Pettifer, S.R.3
Thorne, D.4
Attwood, T.K.5
Vriend, G.6
-
96
-
-
0032870608
-
Improving Macromolecular Electrostatics Calculations
-
Nielsen, J. E.; Andersen, K. V.; Honig, B.; Hooft, R. W.; Klebe, G.; Vriend, G.; Wade, R. C. Improving Macromolecular Electrostatics Calculations Protein Eng., Des. Sel. 1999, 12, 657-662 10.1093/protein/12.8.657
-
(1999)
Protein Eng., Des. Sel.
, vol.12
, pp. 657-662
-
-
Nielsen, J.E.1
Andersen, K.V.2
Honig, B.3
Hooft, R.W.4
Klebe, G.5
Vriend, G.6
Wade, R.C.7
-
97
-
-
0035370422
-
Optimizing the Hydrogen-bond Network in Poisson-Boltzmann Equation-based pK(a) Calculations
-
Nielsen, J. E.; Vriend, G. Optimizing the Hydrogen-bond Network in Poisson-Boltzmann Equation-based pK(a) Calculations Proteins: Struct., Funct., Genet. 2001, 43, 403-412 10.1002/prot.1053
-
(2001)
Proteins: Struct., Funct., Genet.
, vol.43
, pp. 403-412
-
-
Nielsen, J.E.1
Vriend, G.2
-
98
-
-
23144457576
-
H++: A Server for Estimating pKas and Adding Missing Hydrogens to Macromolecules
-
Gordon, J. C.; Myers, J. B.; Folta, T.; Shoja, V.; Heath, L. S.; Onufriev, A. H++: A Server for Estimating pKas and Adding Missing Hydrogens to Macromolecules Nucleic Acids Res. 2005, 33, W368-W371 10.1093/nar/gki464
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W368-W371
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
Onufriev, A.6
-
99
-
-
84864473993
-
H++ 3.0: Automating pK Prediction and the Preparation of Biomolecular Structures for Atomistic Molecular Modeling and Simulations
-
Anandakrishnan, R.; Aguilar, B.; Onufriev, A. V. H++ 3.0: Automating pK Prediction and the Preparation of Biomolecular Structures for Atomistic Molecular Modeling and Simulations Nucleic Acids Res. 2012, 40, W537-W541 10.1093/nar/gks375
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W537-W541
-
-
Anandakrishnan, R.1
Aguilar, B.2
Onufriev, A.V.3
-
100
-
-
0025197061
-
PKa's of Ionizable Groups in Proteins: Atomic Detail from a Eontinuum electrostatic Model
-
Bashford, D.; Karplus, M. pKa's of Ionizable Groups in Proteins: Atomic Detail from a Eontinuum electrostatic Model Biochemistry 1990, 29, 10219-10225 10.1021/bi00496a010
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
101
-
-
0033873929
-
Comparative Protein Structure Modeling of Genes and Genomes
-
Marti-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sanchez, R.; Melo, F.; Sali, A. Comparative Protein Structure Modeling of Genes and Genomes Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291-325 10.1146/annurev.biophys.29.1.291
-
(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
Sali, A.6
-
102
-
-
0033810049
-
Modeling of Loops in Protein Structures
-
Fiser, A.; Do, R. K.; Sali, A. Modeling of Loops in Protein Structures Protein Sci. 2000, 9, 1753-1773 10.1110/ps.9.9.1753
-
(2000)
Protein Sci.
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
103
-
-
0346882663
-
ModLoop: Automated Modeling of Loops in Protein Structures
-
Fiser, A.; Sali, A. ModLoop: Automated Modeling of Loops in Protein Structures Bioinformatics 2003, 19, 2500-25001 10.1093/bioinformatics/btg362
-
(2003)
Bioinformatics
, vol.19
, pp. 2500-25001
-
-
Fiser, A.1
Sali, A.2
-
104
-
-
33747863016
-
ArchPRED: A Template Based Loop Structure Prediction Server
-
Fernandez-Fuentes, N.; Zhai, J.; Fiser, A. ArchPRED: A Template Based Loop Structure Prediction Server Nucleic Acids Res. 2006, 34, W173-W176 10.1093/nar/gkl113
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W173-W176
-
-
Fernandez-Fuentes, N.1
Zhai, J.2
Fiser, A.3
-
105
-
-
84871034858
-
3Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic-Level Energy Minimization
-
Bhattacharya, D.; Cheng, J. 3Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic-Level Energy Minimization Proteins: Struct., Funct., Genet. 2013, 81, 119-131 10.1002/prot.24167
-
(2013)
Proteins: Struct., Funct., Genet.
, vol.81
, pp. 119-131
-
-
Bhattacharya, D.1
Cheng, J.2
-
106
-
-
84983517577
-
-
Gaussian09, Revision D.01; Gaussian, Inc. Wallingford, CT
-
Frisch, M. J.; Trucks, 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; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian09, Revision D.01; Gaussian, Inc.: Wallingford, CT, 2009.
-
(2009)
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
Nakatsuji, H.11
Caricato, M.12
Li, X.13
Hratchian, H.P.14
Izmaylov, A.F.15
Bloino, J.16
Zheng, G.17
Sonnenberg, J.L.18
Hada, M.19
Ehara, M.20
Toyota, K.21
Fukuda, R.22
Hasegawa, J.23
Ishida, M.24
Nakajima, T.25
Honda, Y.26
Kitao, O.27
Nakai, H.28
Vreven, T.29
Montgomery, Jr.J.A.30
Peralta, J.E.31
Ogliaro, F.32
Bearpark, M.33
Heyd, J.J.34
Brothers, E.35
Kudin, K.N.36
Staroverov, V.N.37
Kobayashi, R.38
Normand, J.39
Raghavachari, K.40
Rendell, A.41
Burant, J.C.42
Iyengar, S.S.43
Tomasi, J.44
Cossi, M.45
Rega, N.46
Millam, J.M.47
Klene, M.48
Knox, J.E.49
Cross, J.B.50
Bakken, V.51
Adamo, C.52
Jaramillo, J.53
Gomperts, R.54
Stratmann, R.E.55
Yazyev, O.56
Austin, A.J.57
Cammi, R.58
Pomelli, C.59
Ochterski, J.W.60
Martin, R.L.61
Morokuma, K.62
Zakrzewski, V.G.63
Voth, G.A.64
Salvador, P.65
Dannenberg, J.J.66
Dapprich, S.67
Daniels, A.D.68
Farkas69
Foresman, J.B.70
Ortiz, J.V.71
Cioslowski, J.72
Fox, D.J.73
more..
-
107
-
-
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.; Vorobyov, I.; Mackerell, A. D., Jr. CHARMM General Force Field: A Force Field for Drug-like Molecules Compatible with the CHARMM All-atom Additive Biological Force Fields J. Comput. Chem. 2010, 31, 671-690 10.1002/jcc.21367
-
(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
MacKerell, Jr.A.D.11
-
108
-
-
84871545594
-
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
-
Vanommeslaeghe, K.; MacKerell, A. D., Jr. Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing J. Chem. Inf. Model. 2012, 52, 3144-3154 10.1021/ci300363c
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3144-3154
-
-
Vanommeslaeghe, K.1
MacKerell, Jr.A.D.2
-
109
-
-
84871544678
-
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
-
Vanommeslaeghe, K.; Raman, E. P.; MacKerell, A. D., Jr. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges J. Chem. Inf. Model. 2012, 52, 3155-3168 10.1021/ci3003649
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3155-3168
-
-
Vanommeslaeghe, K.1
Raman, E.P.2
MacKerell, Jr.A.D.3
-
110
-
-
3042524904
-
A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Determining Atom-Centered Charges: The RESP Model
-
Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Determining Atom-Centered 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.D.3
Kollman, P.A.4
-
111
-
-
0000667030
-
Application of RESP charges to Calculate Conformational Energies, Hydrogen Bond Energies and Free Energies of Solvation
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollmann, P. A. Application of RESP charges to Calculate Conformational Energies, Hydrogen Bond Energies and Free Energies of Solvation J. Am. Chem. Soc. 1993, 115, 9620-9631 10.1021/ja00074a030
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollmann, P.A.4
-
112
-
-
84986516411
-
Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derivation for DNA, RNA and Proteins
-
Cieplak, P.; Cornell, W. D.; Bayly, C. I.; Kollman, P. A. Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derivation for DNA, RNA and Proteins J. Comput. Chem. 1995, 16, 1357-1377 10.1002/jcc.540161106
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.I.3
Kollman, P.A.4
-
113
-
-
84887126779
-
Rapid Parameterization of Small Molecules Using the Force Field Toolkit
-
Mayne, C. G.; Saam, J.; Schulten, K.; Tajkhorshid, E.; Gumbart, J. C. Rapid Parameterization of Small Molecules Using the Force Field Toolkit J. Comput. Chem. 2013, 34, 2757-2770 10.1002/jcc.23422
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2757-2770
-
-
Mayne, C.G.1
Saam, J.2
Schulten, K.3
Tajkhorshid, E.4
Gumbart, J.C.5
-
114
-
-
33748538349
-
Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations J. Mol. Graphics Modell. 2006, 25, 247-260 10.1016/j.jmgm.2005.12.005
-
(2006)
J. Mol. Graphics Modell.
, vol.25
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
115
-
-
84865228751
-
ACPYPE - AnteChamber PYthon Parser InterfacE
-
Sousa da Silva, A. W.; Vranken, W. F. ACPYPE-AnteChamber PYthon Parser InterfacE BMC Res. Notes 2012, 5, 367 10.1186/1756-0500-5-367
-
(2012)
BMC Res. Notes
, vol.5
, pp. 367
-
-
Sousa Da Silva, A.W.1
Vranken, W.F.2
-
116
-
-
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
-
117
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
118
-
-
0041784950
-
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616 10.1021/jp973084f
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
119
-
-
0242593434
-
Development and Current Status of the CHARMM Force Field for Nucleic Acids
-
MacKerell, A. D., Jr.; Banavali, N.; Foloppe, N. Development and Current Status of the CHARMM Force Field for Nucleic Acids Biopolymers 2000, 56, 257-65 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
-
(2000)
Biopolymers
, vol.56
, pp. 257-265
-
-
MacKerell, Jr.A.D.1
Banavali, N.2
Foloppe, N.3
-
120
-
-
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
-
121
-
-
84862098170
-
Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics
-
Dixit, A.; Verkhivker, G. M. Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics PLoS One 2012, 7, e37605 10.1371/journal.pone.0037605
-
(2012)
PLoS One
, vol.7
, pp. e37605
-
-
Dixit, A.1
Verkhivker, G.M.2
-
122
-
-
84903398935
-
Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications
-
Blacklock, K.; Verkhivker, G. M. Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications PLoS Comput. Biol. 2014, 10, e1003679 10.1371/journal.pcbi.1003679
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003679
-
-
Blacklock, K.1
Verkhivker, G.M.2
-
123
-
-
0029878720
-
VMD: Visual Molecular Dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38 10.1016/0263-7855(96)00018-5
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
124
-
-
36449003554
-
Constant Pressure Molecular Dynamics Algorithms
-
Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189 10.1063/1.467468
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
125
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593 10.1063/1.470117
-
(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
Pedersen, L.G.6
-
126
-
-
0033104039
-
New Tricks for Modelers from the Crystallography Toolkit: The Particle Mesh Ewald Algorithm and Its Use in Nucleic Acid Simulations
-
Darden, T.; Perera, L.; Li, L.; Pedersen, L. New Tricks for Modelers from the Crystallography Toolkit: The Particle Mesh Ewald Algorithm and Its Use in Nucleic Acid Simulations Structure 1999, 7, R55-R60 10.1016/S0969-2126(99)80033-1
-
(1999)
Structure
, vol.7
, pp. R55-R60
-
-
Darden, T.1
Perera, L.2
Li, L.3
Pedersen, L.4
-
127
-
-
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
-
128
-
-
84883743019
-
Grcarma: A Fully Automated Task-Oriented Interface for the Analysis of Molecular Dynamics Trajectories
-
Koukos, P. I.; Glykos, N. M. Grcarma: A Fully Automated Task-Oriented Interface For the Analysis of Molecular Dynamics Trajectories J. Comput. Chem. 2013, 34, 2310-2312 10.1002/jcc.23381
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2310-2312
-
-
Koukos, P.I.1
Glykos, N.M.2
-
129
-
-
61449106774
-
Principal Component Analysis of Native Ensembles of Biomolecular Structures (PCA-NEST): Insights into Functional Dynamics
-
Yang, L. W.; Eyal, E.; Bahar, I.; Kitao, A. Principal Component Analysis of Native Ensembles of Biomolecular Structures (PCA-NEST): Insights into Functional Dynamics Bioinformatics 2009, 25, 606-614 10.1093/bioinformatics/btp023
-
(2009)
Bioinformatics
, vol.25
, pp. 606-614
-
-
Yang, L.W.1
Eyal, E.2
Bahar, I.3
Kitao, A.4
-
130
-
-
77952938726
-
Global Dynamics of Proteins: Bridging between Structure and Function
-
Bahar, I.; Lezon, T. R.; Yang, L. W.; Eyal, E. Global Dynamics of Proteins: Bridging Between Structure and Function Annu. Rev. Biophys. 2010, 39, 23-42 10.1146/annurev.biophys.093008.131258
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.W.3
Eyal, E.4
-
131
-
-
0345973041
-
Gaussian Dynamics of Folded Proteins
-
Haliloglu, T.; Bahar, I.; Erman, B. Gaussian Dynamics of Folded Proteins Phys. Rev. Lett. 1997, 79, 3090-3093 10.1103/PhysRevLett.79.3090
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 3090-3093
-
-
Haliloglu, T.1
Bahar, I.2
Erman, B.3
-
132
-
-
33747829284
-
OGNM: Online Computation of Structural Dynamics Using the Gaussian Network Model
-
Yang, L. W.; Rader, A. J.; Liu, X.; Jursa, C. J.; Chen, S. C.; Karimi, H. A.; Bahar, I. oGNM: Online Computation of Structural Dynamics Using the Gaussian Network Model Nucleic Acids Res. 2006, 34, W24-W31 10.1093/nar/gkl084
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W24-W31
-
-
Yang, L.W.1
Rader, A.J.2
Liu, X.3
Jursa, C.J.4
Chen, S.C.5
Karimi, H.A.6
Bahar, I.7
-
133
-
-
14844286108
-
Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes
-
Ma, J. Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes Structure 2005, 13, 373-380 10.1016/j.str.2005.02.002
-
(2005)
Structure
, vol.13
, pp. 373-380
-
-
Ma, J.1
-
134
-
-
25844431698
-
Coarse-grained Normal Mode Analysis in Structural Biology
-
Bahar, I.; Rader, A. J. Coarse-grained Normal Mode Analysis in Structural Biology Curr. Opin. Struct. Biol. 2005, 15, 586-592 10.1016/j.sbi.2005.08.007
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
135
-
-
0034029144
-
Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior
-
Keskin, O.; Jernigan, R. L.; Bahar, I. Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior Biophys. J. 2000, 78, 2093-2106 10.1016/S0006-3495(00)76756-7
-
(2000)
Biophys. J.
, vol.78
, pp. 2093-2106
-
-
Keskin, O.1
Jernigan, R.L.2
Bahar, I.3
-
136
-
-
34248159870
-
Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics
-
Rueda, M.; Chacón, P.; Orozco, M. Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics Structure 2007, 15, 565-575 10.1016/j.str.2007.03.013
-
(2007)
Structure
, vol.15
, pp. 565-575
-
-
Rueda, M.1
Chacón, P.2
Orozco, M.3
-
137
-
-
84867313359
-
Measuring and Comparing Structural Fluctuation Patterns in Large Protein Datasets
-
Fuglebakk, E.; Echave, J.; Reuter, N. Measuring and Comparing Structural Fluctuation Patterns in Large Protein Datasets Bioinformatics 2012, 28, 2431-2440 10.1093/bioinformatics/bts445
-
(2012)
Bioinformatics
, vol.28
, pp. 2431-2440
-
-
Fuglebakk, E.1
Echave, J.2
Reuter, N.3
-
138
-
-
25444528449
-
WEBnm@: A web Application for Normal Mode Analyses of Proteins
-
Hollup, S. M.; Salensminde, G.; Reuter, N. WEBnm@: A web Application for Normal Mode Analyses of Proteins BMC Bioinf. 2005, 6, 52 10.1186/1471-2105-6-52
-
(2005)
BMC Bioinf.
, vol.6
, pp. 52
-
-
Hollup, S.M.1
Salensminde, G.2
Reuter, N.3
-
139
-
-
0032533790
-
Analysis of Domain Motions by Approximate Normal Mode Calculations
-
Hinsen, K. Analysis of Domain Motions by Approximate Normal Mode Calculations Proteins: Struct., Funct., Genet. 1998, 33, 417-429 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
-
(1998)
Proteins: Struct., Funct., Genet.
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
140
-
-
0036291145
-
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More than 1000 Mutations
-
Guerois, R.; Nielsen, J. E.; Serrano, L. Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More than 1000 Mutations J. Mol. Biol. 2002, 320, 369-387 10.1016/S0022-2836(02)00442-4
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
141
-
-
34248674895
-
The Stability Effects of Protein Mutations Appear to be Universally Distributed
-
Tokuriki, N.; Stricher, F.; Schymkowitz, J.; Serrano, L.; Tawfik, D. S. The Stability Effects of Protein Mutations Appear to be Universally Distributed J. Mol. Biol. 2007, 369, 1318-1332 10.1016/j.jmb.2007.03.069
-
(2007)
J. Mol. Biol.
, vol.369
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
142
-
-
23144436398
-
The FoldX web Server: An Online Force Field
-
Schymkowitz, J.; Borg, J.; Stricher, F.; Nys, R.; Rousseau, F.; Serrano, L. The FoldX web Server: An Online Force Field Nucleic Acids Res. 2005, 33, W382-W388 10.1093/nar/gki387
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W382-W388
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
143
-
-
79958140522
-
A Graphical Interface for the FoldX Force Field
-
Van Durme, J.; Delgado, J.; Stricher, F.; Serrano, L.; Schymkowitz, J.; Rousseau, F. A Graphical Interface for the FoldX Force Field Bioinformatics 2011, 27, 1711-1712 10.1093/bioinformatics/btr254
-
(2011)
Bioinformatics
, vol.27
, pp. 1711-1712
-
-
Van Durme, J.1
Delgado, J.2
Stricher, F.3
Serrano, L.4
Schymkowitz, J.5
Rousseau, F.6
-
144
-
-
84870051131
-
Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol
-
Christensen, N. J.; Kepp, K. P. Accurate Stabilities of Laccase Mutants Predicted With a Modified FoldX Protocol J. Chem. Inf. Model. 2012, 52, 3028-3042 10.1021/ci300398z
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3028-3042
-
-
Christensen, N.J.1
Kepp, K.P.2
-
145
-
-
84880023622
-
Stability Mechanisms of Laccase Isoforms Using a Modified FoldX Protocol Applicable to Widely Different Proteins
-
Christensen, N. J.; Kepp, K. P. Stability Mechanisms of Laccase Isoforms Using a Modified FoldX Protocol Applicable to Widely Different Proteins J. Chem. Theory Comput. 2013, 9, 3210-3223 10.1021/ct4002152
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3210-3223
-
-
Christensen, N.J.1
Kepp, K.P.2
-
146
-
-
84904803708
-
DUET: A Server for Predicting Effects of Mutations on Protein Stability Using an Integrated Computational Approach
-
Pires, D. E.; Ascher, D. B.; Blundell, T. L. DUET: A Server for Predicting Effects of Mutations on Protein Stability Using an Integrated Computational Approach Nucleic Acids Res. 2014, 42, W314-W319 10.1093/nar/gku411
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W314-W319
-
-
Pires, D.E.1
Ascher, D.B.2
Blundell, T.L.3
-
147
-
-
84893298981
-
MCSM: Predicting the Effects of Mutations in Proteins Using Graph-Based Signatures
-
Pires, D. E.; Ascher, D. B.; Blundell, T. L. mCSM: Predicting the Effects of Mutations in Proteins Using Graph-Based Signatures Bioinformatics 2014, 30, 335-342 10.1093/bioinformatics/btt691
-
(2014)
Bioinformatics
, vol.30
, pp. 335-342
-
-
Pires, D.E.1
Ascher, D.B.2
Blundell, T.L.3
-
148
-
-
79959942908
-
SDM - A Server for Predicting Effects of Mutations on Protein Stability and Malfunction
-
Worth, C. L.; Preissner, R.; Blundell, T. L. SDM-A Server for Predicting Effects of Mutations on Protein Stability and Malfunction Nucleic Acids Res. 2011, 39, W215-W222 10.1093/nar/gkr363
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W215-W222
-
-
Worth, C.L.1
Preissner, R.2
Blundell, T.L.3
-
149
-
-
0032560959
-
Continuum Solvent Studies of the Stability of DNA, RNA and Phosphoramidate-DNA Helices
-
Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120, 9401-9409 10.1021/ja981844+
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
150
-
-
0034521981
-
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., 3rd. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Acc. Chem. Res. 2000, 33, 889-897 10.1021/ar000033j
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
151
-
-
84928313330
-
The MM/PBSA and MM/GBSA Methods to Estimate Ligand-Binding Affinities
-
Genheden, S.; Ryde, U. The MM/PBSA and MM/GBSA Methods to Estimate Ligand-Binding Affinities Expert Opin. Drug Discovery 2015, 10, 449-461 10.1517/17460441.2015.1032936
-
(2015)
Expert Opin. Drug Discovery
, vol.10
, pp. 449-461
-
-
Genheden, S.1
Ryde, U.2
-
152
-
-
0033568644
-
Computational Alanine Scanning to Probe Protein-Protein Interactions: A Novel Approach to Evaluate Binding Free Energies
-
Massova, I.; Kollman, P. A. Computational Alanine Scanning to Probe Protein-Protein Interactions: A Novel Approach to Evaluate Binding Free Energies J. Am. Chem. Soc. 1999, 121, 8133-8143 10.1021/ja990935j
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
153
-
-
66149086947
-
Dynamical Networks in tRNA:Protein Complexes
-
Sethi, A.; Eargle, J.; Black, A. A.; Luthey-Schulten, Z. Dynamical Networks in tRNA:Protein Complexes Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 6620-6625 10.1073/pnas.0810961106
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 6620-6625
-
-
Sethi, A.1
Eargle, J.2
Black, A.A.3
Luthey-Schulten, Z.4
-
154
-
-
84945709831
-
Algorithm 97: Shortest Path
-
Floyd, R. W. Algorithm 97: Shortest Path Commun. ACM 1962, 5, 345 10.1145/367766.368168
-
(1962)
Commun. ACM
, vol.5
, pp. 345
-
-
Floyd, R.W.1
-
155
-
-
20444504323
-
Uncovering the Overlapping Community Structure of Complex Networks in Nature and Society
-
Palla, G.; Derényi, I.; Farkas, I.; Vicsek, T. Uncovering the Overlapping Community Structure of Complex Networks in Nature and Society Nature 2005, 435, 814-818 10.1038/nature03607
-
(2005)
Nature
, vol.435
, pp. 814-818
-
-
Palla, G.1
Derényi, I.2
Farkas, I.3
Vicsek, T.4
-
156
-
-
33645830948
-
CFinder: Locating Cliques and Overlapping Modules in Biological Networks
-
Adamcsek, B.; Palla, G.; Farkas, I. J.; Derényi, I.; Vicsek, T. CFinder: Locating Cliques and Overlapping Modules in Biological Networks Bioinformatics 2006, 22, 1021-1023 10.1093/bioinformatics/btl039
-
(2006)
Bioinformatics
, vol.22
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derényi, I.4
Vicsek, T.5
-
157
-
-
33947393946
-
Locating the Active Sites of Enzymes Using Mechanical Properties
-
Sacquin-Mora, S.; Laforet, E.; Lavery, R. Locating the Active Sites of Enzymes Using Mechanical Properties Proteins: Struct., Funct., Genet. 2007, 67, 350-359 10.1002/prot.21353
-
(2007)
Proteins: Struct., Funct., Genet.
, vol.67
, pp. 350-359
-
-
Sacquin-Mora, S.1
Laforet, E.2
Lavery, R.3
-
158
-
-
78649295907
-
Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress
-
Sacquin-Mora, S.; Delalande, O.; Baaden, M. Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress Biophys. J. 2010, 99, 3412-3419 10.1016/j.bpj.2010.09.026
-
(2010)
Biophys. J.
, vol.99
, pp. 3412-3419
-
-
Sacquin-Mora, S.1
Delalande, O.2
Baaden, M.3
-
159
-
-
63549104682
-
Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full Length Dimer
-
Morra, G.; Verkhivker, G.; Colombo, G. Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full Length Dimer PLoS Comput. Biol. 2009, 5, e1000323 10.1371/journal.pcbi.1000323
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000323
-
-
Morra, G.1
Verkhivker, G.2
Colombo, G.3
-
160
-
-
84888606976
-
Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study
-
Blacklock, K.; Verkhivker, G. Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study PLoS One 2013, 8, e71936 10.1371/journal.pone.0071936
-
(2013)
PLoS One
, vol.8
, pp. e71936
-
-
Blacklock, K.1
Verkhivker, G.2
-
161
-
-
13044272912
-
Automated Analysis of Interatomic Contacts in Proteins
-
Sobolev, V.; Sorokine, A.; Prilusky, J.; Abola, E. E.; Edelman, M. Automated Analysis of Interatomic Contacts in Proteins Bioinformatics 1999, 15, 327-332 10.1093/bioinformatics/15.4.327
-
(1999)
Bioinformatics
, vol.15
, pp. 327-332
-
-
Sobolev, V.1
Sorokine, A.2
Prilusky, J.3
Abola, E.E.4
Edelman, M.5
-
162
-
-
44649110104
-
Structural Basis for the Cooperation of Hsp70 and Hsp110 Chaperones in Protein Folding
-
Polier, S.; Dragovic, Z.; Hartl, F. U.; Bracher, A. Structural Basis for the Cooperation of Hsp70 and Hsp110 Chaperones in Protein Folding Cell 2008, 133, 1068-10679 10.1016/j.cell.2008.05.022
-
(2008)
Cell
, vol.133
, pp. 1068-10679
-
-
Polier, S.1
Dragovic, Z.2
Hartl, F.U.3
Bracher, A.4
-
163
-
-
84863155446
-
Unique Peptide Substrate Binding Properties of 110-kDa Heat-Shock Protein (Hsp110) Determine Its Distinct Chaperone Activity
-
Xu, X.; Sarbeng, E. B.; Vorvis, C.; Kumar, D. P.; Zhou, L.; Liu, Q. Unique Peptide Substrate Binding Properties of 110-kDa Heat-Shock Protein (Hsp110) Determine Its Distinct Chaperone Activity J. Biol. Chem. 2012, 287, 5661-5672 10.1074/jbc.M111.275057
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 5661-5672
-
-
Xu, X.1
Sarbeng, E.B.2
Vorvis, C.3
Kumar, D.P.4
Zhou, L.5
Liu, Q.6
-
164
-
-
33748363077
-
Dynamically Driven Protein Allostery
-
Popovych, N.; Sun, S.; Ebright, R. H.; Kalodimos, C. G. Dynamically Driven Protein Allostery Nat. Struct. Mol. Biol. 2006, 13, 831-838 10.1038/nsmb1132
-
(2006)
Nat. Struct. Mol. Biol.
, vol.13
, pp. 831-838
-
-
Popovych, N.1
Sun, S.2
Ebright, R.H.3
Kalodimos, C.G.4
-
165
-
-
84864651001
-
Protein Activity Regulation by Conformational Entropy
-
Tzeng, S. R.; Kalodimos, C. G. Protein Activity Regulation by Conformational Entropy Nature 2012, 488, 236-240 10.1038/nature11271
-
(2012)
Nature
, vol.488
, pp. 236-240
-
-
Tzeng, S.R.1
Kalodimos, C.G.2
-
166
-
-
33947495228
-
Do All pieces Make A Whole? Thiele Cumulants and the Free-Energy Decomposition
-
Bren, M.; Florián, J.; Bren, U.; Mavri, J. Do All pieces Make A Whole? Thiele Cumulants and The Free-Energy Decomposition Theor. Chem. Acc. 2007, 117, 535-540 10.1007/s00214-007-0264-z
-
(2007)
Theor. Chem. Acc.
, vol.117
, pp. 535-540
-
-
Bren, M.1
Florián, J.2
Bren, U.3
Mavri, J.4
-
167
-
-
33746508990
-
Decomposition of the Solvation Free Energies of Deoxyribonucleoside Triphosphates Using the Free Energy Perturbation Method
-
Bren, U.; Martínek, V.; Florián, J. Decomposition of the Solvation Free Energies of Deoxyribonucleoside Triphosphates Using The Free Energy Perturbation Method J. Phys. Chem. B 2006, 110, 12782-12788 10.1021/jp056623m
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12782-12788
-
-
Bren, U.1
Martínek, V.2
Florián, J.3
-
168
-
-
79952588669
-
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free energy Calculations Based on Molecular Dynamics Simulations
-
Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free energy Calculations Based on Molecular Dynamics Simulations J. Chem. Inf. Model. 2011, 51, 69-82 10.1021/ci100275a
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 69-82
-
-
Hou, T.1
Wang, J.2
Li, Y.3
Wang, W.4
-
169
-
-
84904438047
-
Assessing the Performance of MM/PBSA and MM/GBSA Methods. 4. Accuracies of MM/PBSA and MM/GBSA Methodologies Evaluated by Various Simulation Protocols Using PDBbind Data Set
-
Sun, H.; Li, Y.; Tian, S.; Xu, L.; Hou, T. Assessing the Performance of MM/PBSA and MM/GBSA Methods. 4. Accuracies of MM/PBSA and MM/GBSA Methodologies Evaluated by Various Simulation Protocols Using PDBbind Data Set Phys. Chem. Chem. Phys. 2014, 16, 16719-16729 10.1039/C4CP01388C
-
(2014)
Phys. Chem. Chem. Phys.
, vol.16
, pp. 16719-16729
-
-
Sun, H.1
Li, Y.2
Tian, S.3
Xu, L.4
Hou, T.5
-
170
-
-
84893847867
-
Molecular Dynamics Simulation Studies on the Positive Cooperativity of the Kemptide Substrate with Protein Kinase A Induced by the ATP Ligand
-
Li, C.; Ma, N.; Wang, Y.; Wang, Y.; Chen, G. Molecular Dynamics Simulation Studies on the Positive Cooperativity of the Kemptide Substrate with Protein Kinase A Induced by the ATP Ligand J. Phys. Chem. B 2014, 118, 1273-1287 10.1021/jp411111g
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 1273-1287
-
-
Li, C.1
Ma, N.2
Wang, Y.3
Wang, Y.4
Chen, G.5
-
171
-
-
84862884578
-
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations
-
Bren, U.; Oostenbrink, C. J. Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations J. Chem. Inf. Model. 2012, 52, 1573-1582 10.1021/ci300118x
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1573-1582
-
-
Bren, U.1
Oostenbrink, C.J.2
-
172
-
-
84918524642
-
Cooperative Binding of Aflatoxin B1 by Cytochrome P450 3A4: A Computational Study
-
Bren, U.; Fuchs, J. E.; Oostenbrink, C. Cooperative Binding of Aflatoxin B1 by Cytochrome P450 3A4: A Computational Study Chem. Res. Toxicol. 2014, 27, 2136-2147 10.1021/tx5004062
-
(2014)
Chem. Res. Toxicol.
, vol.27
, pp. 2136-2147
-
-
Bren, U.1
Fuchs, J.E.2
Oostenbrink, C.3
-
173
-
-
0034765285
-
Delineation of the Allosteric Mechanism of a Cytidylyltransferase Exhibiting Negative Cooperativity
-
Stevens, S. Y.; Sanker, S.; Kent, C.; Zuiderweg, E. R. Delineation of the Allosteric Mechanism of a Cytidylyltransferase Exhibiting Negative Cooperativity Nat. Struct. Biol. 2001, 8, 947-952 10.1038/nsb1101-947
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 947-952
-
-
Stevens, S.Y.1
Sanker, S.2
Kent, C.3
Zuiderweg, E.R.4
-
174
-
-
77950521526
-
Lactose Binding to Galectin-1 Modulates Structural dynamics, Increases Conformational Entropy, and Occurs with Apparent Negative Cooperativity
-
Nesmelova, I. V.; Ermakova, E.; Daragan, V. A.; Pang, M.; Menendez, M.; Lagartera, L.; Solis, D.; Baum, L. G.; Mayo, K. H. Lactose Binding to Galectin-1 Modulates Structural dynamics, Increases Conformational Entropy, and Occurs with Apparent Negative Cooperativity J. Mol. Biol. 2010, 397, 1209-1230 10.1016/j.jmb.2010.02.033
-
(2010)
J. Mol. Biol.
, vol.397
, pp. 1209-1230
-
-
Nesmelova, I.V.1
Ermakova, E.2
Daragan, V.A.3
Pang, M.4
Menendez, M.5
Lagartera, L.6
Solis, D.7
Baum, L.G.8
Mayo, K.H.9
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