-
2
-
-
0034676455
-
Surfing the p53 Network
-
Vogelstein, B.; Lane, D.; Levine, A. J. Surfing the p53 Network Nature 2000, 408, 307-310
-
(2000)
Nature
, vol.408
, pp. 307-310
-
-
Vogelstein, B.1
Lane, D.2
Levine, A.J.3
-
3
-
-
0031987277
-
Regulation of p53 Downstream Genes
-
El-Deiry, W. S. Regulation of p53 Downstream Genes Semin. Cancer Biol. 1998, 8, 345-357
-
(1998)
Semin. Cancer Biol.
, vol.8
, pp. 345-357
-
-
El-Deiry, W.S.1
-
4
-
-
47649096991
-
Structural Biology of the Tumor Suppressor p53
-
Joerger, A. C.; Fersht, A. R. Structural Biology of the Tumor Suppressor p53 Annu. Rev. Biochem. 2008, 77, 557-582
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 557-582
-
-
Joerger, A.C.1
Fersht, A.R.2
-
5
-
-
14044251523
-
The C Terminus of p53 Family Proteins Is a Cell Fate Determinant
-
Harms, K. L.; Chen, X. The C Terminus of p53 Family Proteins Is a Cell Fate Determinant Mol. Cell. Biol. 2005, 25, 2014-2030
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 2014-2030
-
-
Harms, K.L.1
Chen, X.2
-
6
-
-
0033521143
-
Conformation and Molecular Basis for Induction of Apoptosis by a p53 C-terminal Peptide in Human Cancer Cells
-
Kim, A. L.; Raffo, A. J.; Brandt-Rauf, P. W.; Pincus, M. R.; Monaco, R.; Abarzua, P.; Fine, R. L. Conformation and Molecular Basis for Induction of Apoptosis by a p53 C-terminal Peptide in Human Cancer Cells J. Biol. Chem. 1999, 274, 34924-34931
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 34924-34931
-
-
Kim, A.L.1
Raffo, A.J.2
Brandt-Rauf, P.W.3
Pincus, M.R.4
Monaco, R.5
Abarzua, P.6
Fine, R.L.7
-
7
-
-
8644241631
-
P53 Linear Diffusion along DNA Requires Its C Terminus
-
McKinney, K.; Mattia, M.; Gottifredi, V.; Prives, C. p53 Linear Diffusion along DNA Requires Its C Terminus Mol. Cell 2004, 16, 413-424
-
(2004)
Mol. Cell
, vol.16
, pp. 413-424
-
-
McKinney, K.1
Mattia, M.2
Gottifredi, V.3
Prives, C.4
-
8
-
-
46749108829
-
Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability
-
Tafvizi, A.; Huang, F.; Leith, J. S.; Fersht, A. R.; Mirny, L. A.; van Oijen, A. M. Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability Biophys. J. 2008, 95, L01-L03
-
(2008)
Biophys. J.
, vol.95
-
-
Tafvizi, A.1
Huang, F.2
Leith, J.S.3
Fersht, A.R.4
Mirny, L.A.5
Van Oijen, A.M.6
-
9
-
-
1442330508
-
Acetylation of p53 Augments its Site-Specific DNA Binding Both in Vitro and in Vivo
-
Luo, J.; Li, M.; Tang, Y.; Laskowska, M.; Roeder, R. G.; Gu, W. Acetylation of p53 Augments its Site-Specific DNA Binding Both in Vitro and in Vivo Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 2259-2264
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 2259-2264
-
-
Luo, J.1
Li, M.2
Tang, Y.3
Laskowska, M.4
Roeder, R.G.5
Gu, W.6
-
10
-
-
17044391806
-
Modulation of Binding of DNA to the C-Terminal Domain of p53 by Acetylation
-
Friedler, A.; Veprintsev, D. B.; Freund, S. M. V.; von Glos, K. I.; Fersht, A. R. Modulation of Binding of DNA to the C-Terminal Domain of p53 by Acetylation Structure 2005, 13, 629-636
-
(2005)
Structure
, vol.13
, pp. 629-636
-
-
Friedler, A.1
Veprintsev, D.B.2
Freund, S.M.V.3
Von Glos, K.I.4
Fersht, A.R.5
-
11
-
-
33847674391
-
RNA-p53 Interactions in Vitro
-
Riley, K. J.-L.; Ramirez-Alvarado, M.; Maher, L. J., III. RNA-p53 Interactions in Vitro Biochemistry 2007, 46, 2480-2487
-
(2007)
Biochemistry
, vol.46
, pp. 2480-2487
-
-
Riley, K.J.-L.1
Ramirez-Alvarado, M.2
Maher III, L.J.3
-
12
-
-
0030996361
-
Synergistic Activation of Transcription by CBP and p53
-
Gu, W.; Shi, X.-L.; Roeder, R. G. Synergistic Activation of Transcription by CBP and p53 Nature 1997, 387, 819-823
-
(1997)
Nature
, vol.387
, pp. 819-823
-
-
Gu, W.1
Shi, X.-L.2
Roeder, R.G.3
-
13
-
-
0034881964
-
Transcriptional Regulation by p53 through Intrinsic DNA/Chromatin Binding and Site-Directed Cofactor Recruitment
-
Espinosa, J. M.; Emerson, B. M. Transcriptional Regulation by p53 through Intrinsic DNA/Chromatin Binding and Site-Directed Cofactor Recruitment Mol. Cell 2001, 8, 57-69
-
(2001)
Mol. Cell
, vol.8
, pp. 57-69
-
-
Espinosa, J.M.1
Emerson, B.M.2
-
14
-
-
10744233648
-
Structural Mechanism of the Bromodomain of the Coactivator CBP in p53 Transcriptional Activation
-
Mujtaba, S.; He, Y.; Zeng, L.; Yan, S.; Plotnikova, O.; Sachchidanand; Sanchez, R.; Zeleznik-Le, N. J.; Ronai, Z. e.; Zhou, M.-M. Structural Mechanism of the Bromodomain of the Coactivator CBP in p53 Transcriptional Activation Mol. Cell 2004, 13, 251-263
-
(2004)
Mol. Cell
, vol.13
, pp. 251-263
-
-
Mujtaba, S.1
He, Y.2
Zeng, L.3
Yan, S.4
Plotnikova, O.5
Sachchidanand6
Sanchez, R.7
Zeleznik-Le, N.J.8
Zhou, M.-M.9
-
15
-
-
16344368267
-
Proteins of the S100 Family Regulate the Oligomerization of p53 Tumor Suppressor
-
Fernandez-Fernandez, M. R.; Veprintsev, D. B.; Fersht, A. R. Proteins of the S100 Family Regulate the Oligomerization of p53 Tumor Suppressor Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 4735-4740
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 4735-4740
-
-
Fernandez-Fernandez, M.R.1
Veprintsev, D.B.2
Fersht, A.R.3
-
16
-
-
52949152903
-
Members of the S100 Family Bind p53 in Two Distinct Ways
-
Fernandez-Fernandez, M. R.; Rutherford, T. J.; Fersht, A. R. Members of the S100 Family Bind p53 in Two Distinct Ways Protein Sci. 2008, 17, 1663-1670
-
(2008)
Protein Sci.
, vol.17
, pp. 1663-1670
-
-
Fernandez-Fernandez, M.R.1
Rutherford, T.J.2
Fersht, A.R.3
-
17
-
-
0030797585
-
Activation of p53 Sequence-Specific DNA Binding by Acetylation of the p53 C-Terminal Domain
-
Gu, W.; Roeder, R. G. Activation of p53 Sequence-Specific DNA Binding by Acetylation of the p53 C-Terminal Domain Cell 1997, 90, 595-606
-
(1997)
Cell
, vol.90
, pp. 595-606
-
-
Gu, W.1
Roeder, R.G.2
-
18
-
-
0035943733
-
Regulation of Ubiquitination and Degradation of p53 in Unstressed Cells through C-terminal Phosphorylation
-
Chernov, M. V.; Bean, L. J. H.; Lerner, N.; Stark, G. R. Regulation of Ubiquitination and Degradation of p53 in Unstressed Cells through C-terminal Phosphorylation J. Biol. Chem. 2001, 276, 31819-31824
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 31819-31824
-
-
Chernov, M.V.1
Bean, L.J.H.2
Lerner, N.3
Stark, G.R.4
-
19
-
-
9244247669
-
Regulation of p53 Activity through Lysine Methylation
-
Chuikov, S.; Kurash, J. K.; Wilson, J. R.; Xiao, B.; Justin, N.; Ivanov, G. S.; McKinney, K.; Tempst, P.; Prives, C.; Gamblin, S. J.; Bariev, N. A.; Reinberg, D. Regulation of p53 Activity through Lysine Methylation Nature 2004, 432, 353-360
-
(2004)
Nature
, vol.432
, pp. 353-360
-
-
Chuikov, S.1
Kurash, J.K.2
Wilson, J.R.3
Xiao, B.4
Justin, N.5
Ivanov, G.S.6
McKinney, K.7
Tempst, P.8
Prives, C.9
Gamblin, S.J.10
Bariev, N.A.11
Reinberg, D.12
-
20
-
-
20744448187
-
Functional Analysis of the Roles of Posttranslational Modifications at the p53 C Terminus in Regulating p53 Stability and Activity
-
Feng, L.; Lin, T.; Uranishi, H.; Gu, W.; Xu, Y. Functional Analysis of the Roles of Posttranslational Modifications at the p53 C Terminus in Regulating p53 Stability and Activity Mol. Cell. Biol. 2005, 25, 5389-5395
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 5389-5395
-
-
Feng, L.1
Lin, T.2
Uranishi, H.3
Gu, W.4
Xu, Y.5
-
21
-
-
4944255743
-
Post-Translational Modification of p53 in Tumorigenesis
-
Bode, A. M.; Dong, Z. Post-Translational Modification of p53 in Tumorigenesis Nat. Rev. Cancer 2004, 4, 793-805
-
(2004)
Nat. Rev. Cancer
, vol.4
, pp. 793-805
-
-
Bode, A.M.1
Dong, Z.2
-
22
-
-
33646757232
-
The Complexity of p53 Stabilization and Activation
-
Lavin, M. F.; Gueven, N. The Complexity of p53 Stabilization and Activation Cell Death Differ. 2006, 13, 941-950
-
(2006)
Cell Death Differ.
, vol.13
, pp. 941-950
-
-
Lavin, M.F.1
Gueven, N.2
-
23
-
-
0036415663
-
P53 Contains Large Unstructured Regions in its Native State
-
Bell, S.; Klein, C.; Müller, L.; Hansen, S.; Buchner, J. p53 Contains Large Unstructured Regions in its Native State J. Mol. Biol. 2002, 322, 917-927
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 917-927
-
-
Bell, S.1
Klein, C.2
Müller, L.3
Hansen, S.4
Buchner, J.5
-
24
-
-
20444376186
-
The interplay between structure and function in intrinsically unstructured proteins
-
DOI 10.1016/j.febslet.2005.03.072, PII S0014579305004242
-
Tompa, P. The Interplay between Structure and Function in Intrinsically Unstructured Proteins FEBS Lett. 2005, 579, 3346-3354 (Pubitemid 40804685)
-
(2005)
FEBS Letters
, vol.579
, Issue.15
, pp. 3346-3354
-
-
Tompa, P.1
-
25
-
-
14644435825
-
Intrinsically Unstructured Proteins and Their Functions
-
Dyson, H. J.; Wright, P. E. Intrinsically Unstructured Proteins and Their Functions Nat. Rev. Mol. Cell Biol. 2005, 6, 197-208
-
(2005)
Nat. Rev. Mol. Cell Biol.
, vol.6
, pp. 197-208
-
-
Dyson, H.J.1
Wright, P.E.2
-
26
-
-
27144464910
-
Flexible Nets. The roles of Intrinsic Disorder in Protein Interaction Networks
-
Dunker, A. K.; Cortese, M. S.; Romero, P.; Iakoucheva, L. M.; Uversky, V. N. Flexible Nets. The roles of Intrinsic Disorder in Protein Interaction Networks FEBS J. 2005, 272, 5129-5148
-
(2005)
FEBS J.
, vol.272
, pp. 5129-5148
-
-
Dunker, A.K.1
Cortese, M.S.2
Romero, P.3
Iakoucheva, L.M.4
Uversky, V.N.5
-
27
-
-
0036408751
-
Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins
-
Iakoucheva, L. M.; Brown, C. J.; Lawson, J. D.; Obradovic, Z.; Dunker, A. K. Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins J. Mol. Biol. 2002, 323, 573-584
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 573-584
-
-
Iakoucheva, L.M.1
Brown, C.J.2
Lawson, J.D.3
Obradovic, Z.4
Dunker, A.K.5
-
28
-
-
0033945124
-
Structure of the Negative Regulatory Domain of p53 Bound to S100B(ββ)
-
Rustandi, R. R.; Baldisseri, D. M.; Weber, D. J. Structure of the Negative Regulatory Domain of p53 Bound to S100B(ββ) Nat. Struct. Biol. 2000, 7, 570-575
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 570-575
-
-
Rustandi, R.R.1
Baldisseri, D.M.2
Weber, D.J.3
-
29
-
-
0036753953
-
Structure of a Sir2 Enzyme Bound to an Acetylated p53 Peptide
-
Avalos, J. L.; Celic, I.; Muhammad, S.; Cosgrove, M. S.; Boeke, J. D.; Wolberger, C. Structure of a Sir2 Enzyme Bound to an Acetylated p53 Peptide Mol. Cell 2002, 10, 523-535
-
(2002)
Mol. Cell
, vol.10
, pp. 523-535
-
-
Avalos, J.L.1
Celic, I.2
Muhammad, S.3
Cosgrove, M.S.4
Boeke, J.D.5
Wolberger, C.6
-
30
-
-
0347520938
-
Specificity Determinants of Recruitment Peptides Bound to Phospho-CDK2/Cyclin A
-
Lowe, E. D.; Tews, I.; Cheng, K. Y.; Brown, N. R.; Gul, S.; Noble, M. E. M.; Gamblin, S. J.; Johnson, L. N. Specificity Determinants of Recruitment Peptides Bound to Phospho-CDK2/Cyclin A Biochemistry 2002, 41, 15625-15634
-
(2002)
Biochemistry
, vol.41
, pp. 15625-15634
-
-
Lowe, E.D.1
Tews, I.2
Cheng, K.Y.3
Brown, N.R.4
Gul, S.5
Noble, M.E.M.6
Gamblin, S.J.7
Johnson, L.N.8
-
31
-
-
2142757231
-
Preformed Structural Elements Feature in Partner Recognition by Intrinsically Unstructured Proteins
-
Fuxreiter, M.; Simon, I.; Friedrich, P.; Tompa, P. Preformed Structural Elements Feature in Partner Recognition by Intrinsically Unstructured Proteins J. Mol. Biol. 2004, 338, 1015-1026
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 1015-1026
-
-
Fuxreiter, M.1
Simon, I.2
Friedrich, P.3
Tompa, P.4
-
32
-
-
30344432688
-
Assessing Protein Disorder and Induced Folding
-
Receveur-Bréchot, V.; Bourhis, J.-M.; Uversky, V. N.; Canard, B.; Longhi, S. Assessing Protein Disorder and Induced Folding Proteins 2006, 62, 24-45
-
(2006)
Proteins
, vol.62
, pp. 24-45
-
-
Receveur-Bréchot, V.1
Bourhis, J.-M.2
Uversky, V.N.3
Canard, B.4
Longhi, S.5
-
33
-
-
0036468397
-
Coupling of Folding and Binding for Unstructured Proteins
-
Dyson, H. J.; Wright, P. E. Coupling of Folding and Binding for Unstructured Proteins Curr. Opin. Struct. Biol. 2002, 12, 54-60
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 54-60
-
-
Dyson, H.J.1
Wright, P.E.2
-
34
-
-
67949106402
-
Intrinsically Disordered p53 Extreme C-Terminus Binds to S100B(ββ) through Fly-Casting
-
Chen, J. Intrinsically Disordered p53 Extreme C-Terminus Binds to S100B(ββ) through Fly-Casting J. Am. Chem. Soc. 2009, 131, 2088-2089
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 2088-2089
-
-
Chen, J.1
-
35
-
-
41149177142
-
Modeling the Accessible Conformations of the Intrinsically Unstructured Transactivation Domain of p53
-
Lowry, D. F.; Stancik, A.; Shrestha, R. M.; Daughdrill, G. W. Modeling the Accessible Conformations of the Intrinsically Unstructured Transactivation Domain of p53 Proteins 2008, 71, 587-598
-
(2008)
Proteins
, vol.71
, pp. 587-598
-
-
Lowry, D.F.1
Stancik, A.2
Shrestha, R.M.3
Daughdrill, G.W.4
-
36
-
-
58949101630
-
Leucine-rich Hydrophobic Clusters Promote Folding of the N-terminus of the Intrinsically Disordered Transactivation Domain of p53
-
Espinoza-Fonseca, L. M. Leucine-rich Hydrophobic Clusters Promote Folding of the N-terminus of the Intrinsically Disordered Transactivation Domain of p53 FEBS Lett. 2009, 583, 556-560
-
(2009)
FEBS Lett.
, vol.583
, pp. 556-560
-
-
Espinoza-Fonseca, L.M.1
-
37
-
-
66249090517
-
Modeling the Interaction between the N-terminal Domain of the Tumor Suppressor p53 and Azurin
-
Taranta, M.; Bizzarri, A. R.; Cannistraro, S. Modeling the Interaction Between the N-terminal Domain of the Tumor Suppressor p53 and Azurin J. Mol. Recognit. 2009, 22, 215-222
-
(2009)
J. Mol. Recognit.
, vol.22
, pp. 215-222
-
-
Taranta, M.1
Bizzarri, A.R.2
Cannistraro, S.3
-
38
-
-
66149127273
-
In Silico Improvement of β3-Peptide Inhibitors of p53•hDM2 and p53•hDMX
-
Michel, J.; Harker, E. A.; Tirado-Rives, J.; Jorgensen, W. L.; Schepartz, A. In Silico Improvement of β3-Peptide Inhibitors of p53•hDM2 and p53•hDMX J. Am. Chem. Soc. 2009, 131, 6356-6357
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 6356-6357
-
-
Michel, J.1
Harker, E.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
Schepartz, A.5
-
39
-
-
35348950535
-
Molecular Dynamics Simulations of p53 DNA-Binding Domain
-
Lu, Q.; Tan, Y.-H.; Luo, R. Molecular Dynamics Simulations of p53 DNA-Binding Domain J. Phys. Chem. B 2007, 111, 11538-11545
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 11538-11545
-
-
Lu, Q.1
Tan, Y.-H.2
Luo, R.3
-
40
-
-
34948865835
-
Docking Study and Free Energy Simulation of the Complex between p53 DNA-binding Domain and Azurin
-
De Grandis, V.; Bizzarri, A. R.; Cannistraro, S. Docking Study and Free Energy Simulation of the Complex Between p53 DNA-binding Domain and Azurin J. Mol. Recognit. 2007, 20, 215-226
-
(2007)
J. Mol. Recognit.
, vol.20
, pp. 215-226
-
-
De Grandis, V.1
Bizzarri, A.R.2
Cannistraro, S.3
-
41
-
-
38949105821
-
Molecular Docking Analysis of the Protein-protein Interaction between RelA-associated Inhibitor and the Tumor Suppressor Protein p53 and its Inhibitory Effect on p53 Action
-
Tomoda, K.; Takahashi, N.; Hibi, Y.; Asamitsu, K.; Ishida, H.; Kondo, T.; Yoshitaka, F.; Okamato, T. Molecular Docking Analysis of the Protein-protein Interaction between RelA-associated Inhibitor and the Tumor Suppressor Protein p53 and its Inhibitory Effect on p53 Action Cancer Sci. 2008, 99, 615-622
-
(2008)
Cancer Sci.
, vol.99
, pp. 615-622
-
-
Tomoda, K.1
Takahashi, N.2
Hibi, Y.3
Asamitsu, K.4
Ishida, H.5
Kondo, T.6
Yoshitaka, F.7
Okamato, T.8
-
42
-
-
60749084685
-
Dimerization of the Core Domain of the p53 Family
-
Madhumalar, A.; Jun, L. H.; Lane, D. P.; Verma, C. S. Dimerization of the Core Domain of the p53 Family Cell Cycle 2009, 8, 137-148
-
(2009)
Cell Cycle
, vol.8
, pp. 137-148
-
-
Madhumalar, A.1
Jun, L.H.2
Lane, D.P.3
Verma, C.S.4
-
43
-
-
66749155939
-
Computer Simulations of Peptides from the p53 DNA Binding Domain
-
Khalili, M.; Wales, D. J. Computer Simulations of Peptides from the p53 DNA Binding Domain J. Chem. Theory Comput. 2009, 5, 1380-1392
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1380-1392
-
-
Khalili, M.1
Wales, D.J.2
-
44
-
-
35148819201
-
A Fluid Salt-bridging Cluster and the Stabilization of p53
-
Lwin, T. Z.; Durant, J. J.; Bashford, D. A Fluid Salt-bridging Cluster and the Stabilization of p53 J. Mol. Biol. 2007, 373, 1334-1347
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 1334-1347
-
-
Lwin, T.Z.1
Durant, J.J.2
Bashford, D.3
-
45
-
-
34848859256
-
Theoretical Study on Binding of S100B Protein
-
Gieldon, A.; Mori, M.; Del Conte, R. Theoretical Study on Binding of S100B Protein J. Mol. Model. 2007, 13, 1123-1131
-
(2007)
J. Mol. Model.
, vol.13
, pp. 1123-1131
-
-
Gieldon, A.1
Mori, M.2
Del Conte, R.3
-
46
-
-
67349279571
-
Computational Screening and Design of S100B Ligand to Block S100B-p53 Interaction
-
Withlow, J. L.; Varughese, J. F.; Zhou, Z.; Bartolotti, L. J.; Li, Y. Computational Screening and Design of S100B Ligand to Block S100B-p53 Interaction J. Mol. Graph. Model. 2009, 27, 969-977
-
(2009)
J. Mol. Graph. Model.
, vol.27
, pp. 969-977
-
-
Withlow, J.L.1
Varughese, J.F.2
Zhou, Z.3
Bartolotti, L.J.4
Li, Y.5
-
47
-
-
30744456492
-
Target Structure-Based Discovery of Small Molecules that Block Human p53 and CREB Binding Protein Association
-
Sachchidanand; Resnick-Silverman, L.; Yan, S.; Mutjaba, S.; Liu, W.-j.; Zeng, L.; Manfredi, J. J.; Zhou, M.-M. Target Structure-Based Discovery of Small Molecules that Block Human p53 and CREB Binding Protein Association Chem. Biol. 2006, 13, 81-90
-
(2006)
Chem. Biol.
, vol.13
, pp. 81-90
-
-
Sachchidanand1
Resnick-Silverman, L.2
Yan, S.3
Mutjaba, S.4
Zeng, L.5
Manfredi, J.J.6
Zhou, M.-M.7
-
48
-
-
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
-
(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
-
49
-
-
58049201323
-
-
University of California: San Francisco
-
Case, D. A.; Darden, T. A.; Cheatham III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California: San Francisco, 2008.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
50
-
-
38049034590
-
Comparative Protein Structure Modeling with MODELLER
-
In; John Wiley & Sons, Inc.: New York
-
Eswar, N.; Marti-Renom, M.-A.; Webb, B.; Madhusudhan, M. S.; Eramian, D.; Shen, M.; Pieper, U.; Sali, A. Comparative Protein Structure Modeling With MODELLER. In Current Protocols in Bioinformatics; John Wiley & Sons, Inc.: New York, 2006; Vol. Suppl. 15, pp 5.6.1-5.6.30.
-
(2006)
Current Protocols in Bioinformatics
, vol.15
, Issue.SUPPL.
, pp. 561-5630
-
-
Eswar, N.1
Marti-Renom, M.-A.2
Webb, B.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.6
Pieper, U.7
Sali, A.8
-
51
-
-
0027136282
-
Comparative Protein Modelling by Satisfaction of Spatial Restraints
-
Sali, A.; Blundell, T. L. Comparative Protein Modelling by Satisfaction of Spatial Restraints J. Mol. Biol. 1993, 234, 779-815
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
52
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
DOI 10.1146/annurev.biophys.29.1.291
-
Marti-Renom, M. A.; Stuart, A.; Fiser, A.; Sánchez, R.; Melo, F.; Sali, A. Comparative Protein Structure Modeling of Genes and Genomes Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291-325 (Pubitemid 30599596)
-
(2000)
Annual Review of Biophysics and Biomolecular Structure
, 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
-
53
-
-
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
-
(2000)
Protein Sci.
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
54
-
-
32144432437
-
The SWISS-MODEL Workspace: A Web-based Environment for Protein Structure Homology Modelling
-
Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL Workspace: a Web-based Environment for Protein Structure Homology Modelling Bioinformatics 2006, 22, 195-201
-
(2006)
Bioinformatics
, vol.22
, pp. 195-201
-
-
Arnold, K.1
Bordoli, L.2
Kopp, J.3
Schwede, T.4
-
55
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
56
-
-
4444282928
-
A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6
-
Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1657
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1657
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
57
-
-
0003633496
-
-
D. Reidel Publishing Co.: Dordrecht, The Netherlands
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Intermolecular Forces, Interaction Models for Water in Relation to Protein Hydration; D. Reidel Publishing Co.: Dordrecht, The Netherlands, 1981.
-
(1981)
Intermolecular Forces, Interaction Models for Water in Relation to Protein Hydration
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
58
-
-
36248975150
-
-
version 4.0; Department of Biophysical Chemistry, University of Groningen: Groningen, The Netherlands
-
van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhobb, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual, version 4.0; Department of Biophysical Chemistry, University of Groningen: Groningen, The Netherlands, 2005; www.gromacs.org.
-
(2005)
Gromacs User Manual
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Van Buuren, A.R.4
Apol, E.5
Meulenhobb, P.J.6
Tieleman, D.P.7
Sijbers, A.L.T.M.8
Feenstra, K.A.9
Van Drunen, R.10
Berendsen, H.J.C.11
-
59
-
-
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, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
60
-
-
0000388705
-
LINCS: A Linear Constraint Solver for Molecular Simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
61
-
-
33846823909
-
Particle Mesh Ewald: An N-log(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. G. Particle Mesh Ewald: An N-log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.G.3
-
62
-
-
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
-
(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
-
63
-
-
84943502952
-
A Molecular Dynamics Method for Simulations in the Canonical Ensemble
-
Nosé, S. A Molecular Dynamics Method for Simulations in the Canonical Ensemble Mol. Phys. 1984, 52, 255-268
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
64
-
-
0001538909
-
Canonical Dynamics: Equilibrium Phase-Space Distributions
-
Hoover, W. G. Canonical Dynamics: Equilibrium Phase-Space Distributions Phys. Rev. A 1985, 31, 1695-1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
65
-
-
0019707626
-
Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method
-
Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method J. Appl. Phys. 1981, 52, 7182-7190
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
66
-
-
84926811618
-
Constant Pressure Molecular Dynamics for Molecular Systems
-
Nosé, S.; Klein, M. L. Constant Pressure Molecular Dynamics for Molecular Systems Mol. Phys. 1983, 50, 1055-1076
-
(1983)
Mol. Phys.
, vol.50
, pp. 1055-1076
-
-
Nosé, S.1
Klein, M.L.2
-
67
-
-
85067751744
-
-
http://www.arc.vt.edu/arc/SystemX/.
-
-
-
-
68
-
-
0020997912
-
Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features
-
Kabsch, W.; Sander, C. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features Biopolymers 1983, 22, 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
69
-
-
77958071288
-
-
Center for Coastal and Land-Margin Research Oregon Graduate Institute of Science and Technology: Beaverton, OR
-
Turner, P. J. Grace; Center for Coastal and Land-Margin Research Oregon Graduate Institute of Science and Technology: Beaverton, OR, 2008.
-
(2008)
Grace
-
-
Turner, P.J.1
-
71
-
-
4444221565
-
UCSF Chimera-A Visualization System for Exploratory Research and Analysis
-
Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera-A Visualization System for Exploratory Research and Analysis J. Comput. Chem. 2004, 25, 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Greenblatt, D.M.4
Meng, E.C.5
Ferrin, T.E.6
-
72
-
-
0032101346
-
Essential Spaced Defined by NMR Structure Ensembles and Molecular Dynamics Simulation Show Significant Overlap
-
Abseher, R.; Horstink, L.; Hilbers, C. W.; Nilges, M. Essential Spaced Defined by NMR Structure Ensembles and Molecular Dynamics Simulation Show Significant Overlap Proteins 1998, 31, 370-382
-
(1998)
Proteins
, vol.31
, pp. 370-382
-
-
Abseher, R.1
Horstink, L.2
Hilbers, C.W.3
Nilges, M.4
-
73
-
-
0033167995
-
Exploring the Dynamic Information Content of a Protein NMR Structure: Comparison of a Molecular Dynamics Simulation with the NMR and X-Ray Structures of Escherichia coli Ribonuclease HI
-
Philippopoulos, M.; Lim, C. Exploring the Dynamic Information Content of a Protein NMR Structure: Comparison of a Molecular Dynamics Simulation With the NMR and X-Ray Structures of Escherichia coli Ribonuclease HI Proteins 1999, 36, 87-110
-
(1999)
Proteins
, vol.36
, pp. 87-110
-
-
Philippopoulos, M.1
Lim, C.2
-
74
-
-
53849128197
-
Multiple Peptide Conformations Five Rise to Similar Binding Affinities: Molecular Simulations of p53-MDM2
-
Dastidar, S. G.; Lane, D. P.; Verma, C. S. Multiple Peptide Conformations Five Rise to Similar Binding Affinities: Molecular Simulations of p53-MDM2 J. Am. Chem. Soc. 2008, 130, 13514-13515
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 13514-13515
-
-
Dastidar, S.G.1
Lane, D.P.2
Verma, C.S.3
-
75
-
-
71549116815
-
Modulation of p53 Binding to MDM2: Computational Studies Reveal Important Roles of Tyr100
-
Dastidar, S. G.; Lane, D. P.; Verma, C. S. Modulation of p53 Binding to MDM2: Computational Studies Reveal Important Roles of Tyr100 BMC Bioinf. 2009, 10 (Suppl 15) S6
-
(2009)
BMC Bioinf.
, vol.10
, Issue.SUPPL. 15
, pp. 6
-
-
Dastidar, S.G.1
Lane, D.P.2
Verma, C.S.3
-
76
-
-
77949261530
-
Forces Mediating Protein-Protein Interactions: A Computational Stude of p53 "approaching" MDM2
-
Dastidar, S. G.; Madhumalar, A.; Fuentes, G.; Lane, D. P.; Verma, C. S. Forces Mediating Protein-Protein Interactions: A Computational Stude of p53 "Approaching" MDM2 Theor. Chem. Acc. 2010, 125, 621-635
-
(2010)
Theor. Chem. Acc.
, vol.125
, pp. 621-635
-
-
Dastidar, S.G.1
Madhumalar, A.2
Fuentes, G.3
Lane, D.P.4
Verma, C.S.5
-
77
-
-
0034255123
-
Speeding Molecular Recognition by Using the Folding Funnel: The Fly-Casting Mechanism
-
Shoemaker, B. A.; Portman, J. J.; Wolynes, P. G. Speeding Molecular Recognition by Using the Folding Funnel: The Fly-Casting Mechanism Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8868-8873
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 8868-8873
-
-
Shoemaker, B.A.1
Portman, J.J.2
Wolynes, P.G.3
-
78
-
-
0026683468
-
Entropic Stabilization of a Mutant Human Lysozyme Induced by Calcium Binding
-
Kuroki, R.; Kawakita, S.; Nakamura, H.; Yutani, K. Entropic Stabilization of a Mutant Human Lysozyme Induced by Calcium Binding Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 6803-6807
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 6803-6807
-
-
Kuroki, R.1
Kawakita, S.2
Nakamura, H.3
Yutani, K.4
-
79
-
-
0029908925
-
Catalysis by Entropic Guidance from Enzymes
-
Young, L.; Post, C. B. Catalysis by Entropic Guidance from Enzymes Biochemistry 1996, 35, 15129-15133
-
(1996)
Biochemistry
, vol.35
, pp. 15129-15133
-
-
Young, L.1
Post, C.B.2
-
80
-
-
0031922657
-
Conformational Dynamics and Enzyme Activity
-
Yon, J. M.; Perahia, D.; Ghélis, C. Conformational Dynamics and Enzyme Activity Biochemie 1998, 80, 33-42
-
(1998)
Biochemie
, vol.80
, pp. 33-42
-
-
Yon, J.M.1
Perahia, D.2
Ghélis, C.3
|