-
1
-
-
16244375578
-
The overexpression of specialized DNA polymerases in cancer
-
Albertella MR, Lau A, O'Connor MJ, (2005) The overexpression of specialized DNA polymerases in cancer. DNA Repair 4: 583-593.
-
(2005)
DNA Repair
, vol.4
, pp. 583-593
-
-
Albertella, M.R.1
Lau, A.2
O'Connor, M.J.3
-
3
-
-
34547195827
-
The E295K DNA polymerase beta gastric cancer-associated variant interferes with base excision repair and induces cellular transformation
-
Lang TM, Dalal S, Chikova A, DiMaio D, Sweasy JB, (2007) The E295K DNA polymerase beta gastric cancer-associated variant interferes with base excision repair and induces cellular transformation. Molecular and Cellular Biology 27: 5587-5596.
-
(2007)
Molecular and Cellular Biology
, vol.27
, pp. 5587-5596
-
-
Lang, T.M.1
Dalal, S.2
Chikova, A.3
DiMaio, D.4
Sweasy, J.B.5
-
4
-
-
34250878426
-
Expandable DNA repeats and human disease
-
Mirkin SM, (2007) Expandable DNA repeats and human disease. Nature 447: 932-940.
-
(2007)
Nature
, vol.447
, pp. 932-940
-
-
Mirkin, S.M.1
-
5
-
-
84891727362
-
The D160N gastric cancer-associated variant of DNA polymerase beta induces cellular transformation and genomic instability
-
Sweasy JB, Donigan K, (2008) The D160N gastric cancer-associated variant of DNA polymerase beta induces cellular transformation and genomic instability. Environmental and Molecular Mutagenesis 49: 542-542.
-
(2008)
Environmental and Molecular Mutagenesis
, vol.49
, pp. 542
-
-
Sweasy, J.B.1
Donigan, K.2
-
6
-
-
70350504453
-
The DNA-damage response in human biology and disease
-
Jackson SP, Bartek J, (2009) The DNA-damage response in human biology and disease. Nature 461: 1071-1078.
-
(2009)
Nature
, vol.461
, pp. 1071-1078
-
-
Jackson, S.P.1
Bartek, J.2
-
8
-
-
79952743209
-
Systematic Biochemical Analysis of Somatic Missense Mutations in DNA Polymerase beta Found in Prostate Cancer Reveal Alteration of Enzymatic Function
-
An CL, Chen DS, Makridakis NM, (2011) Systematic Biochemical Analysis of Somatic Missense Mutations in DNA Polymerase beta Found in Prostate Cancer Reveal Alteration of Enzymatic Function. Human Mutation 32: 415-423.
-
(2011)
Human Mutation
, vol.32
, pp. 415-423
-
-
An, C.L.1
Chen, D.S.2
Makridakis, N.M.3
-
10
-
-
84863614548
-
Colon Cancer-associated DNA Polymerase beta Variant Induces Genomic Instability and Cellular Transformation
-
Nemec AA, Donigan KA, Murphy DL, Jaeger J, Sweasy JB, (2012) Colon Cancer-associated DNA Polymerase beta Variant Induces Genomic Instability and Cellular Transformation. Journal of Biological Chemistry 287: 23840-23849.
-
(2012)
Journal of Biological Chemistry
, vol.287
, pp. 23840-23849
-
-
Nemec, A.A.1
Donigan, K.A.2
Murphy, D.L.3
Jaeger, J.4
Sweasy, J.B.5
-
12
-
-
84873866621
-
Biological and Therapeutic Relevance of Nonreplicative DNA Polymerases to Cancer
-
Parsons JL, Nicolay NH, Sharma RA, (2012) Biological and Therapeutic Relevance of Nonreplicative DNA Polymerases to Cancer. Antioxidants & Redox Signaling 18: 851-73.
-
(2012)
Antioxidants & Redox Signaling
, vol.18
, pp. 851-873
-
-
Parsons, J.L.1
Nicolay, N.H.2
Sharma, R.A.3
-
13
-
-
84855827214
-
Biological relevance of DNA polymerase beta and translesion synthesis polymerases to cancer and its treatment
-
Nicolay NH, Helleday T, Sharma RA, (2012) Biological relevance of DNA polymerase beta and translesion synthesis polymerases to cancer and its treatment. Current molecular pharmacology 5: 54-67.
-
(2012)
Current Molecular Pharmacology
, vol.5
, pp. 54-67
-
-
Nicolay, N.H.1
Helleday, T.2
Sharma, R.A.3
-
14
-
-
0033581011
-
DNA polymerases: structural diversity and common mechanisms
-
Steitz TA, (1999) DNA polymerases: structural diversity and common mechanisms. J Biol Chem 274: 17395-17398.
-
(1999)
J Biol Chem
, vol.274
, pp. 17395-17398
-
-
Steitz, T.A.1
-
15
-
-
2342419732
-
DNA replication fidelity
-
Kunkel TA, (2004) DNA replication fidelity. J Biol Chem 279: 16895-16898.
-
(2004)
J Biol Chem
, vol.279
, pp. 16895-16898
-
-
Kunkel, T.A.1
-
16
-
-
58549094699
-
Distribution and roles of X-family DNA polymerases in eukaryotes
-
Uchiyama Y, Takeuchi R, Kodera H, Sakaguchi K, (2009) Distribution and roles of X-family DNA polymerases in eukaryotes. Biochimie 91: 165-170.
-
(2009)
Biochimie
, vol.91
, pp. 165-170
-
-
Uchiyama, Y.1
Takeuchi, R.2
Kodera, H.3
Sakaguchi, K.4
-
17
-
-
0035158355
-
Highly frequent frameshift DNA synthesis by human DNA polymerase mu
-
Zhang Y, Wu X, Yuan F, Xie Z, Wang Z, (2001) Highly frequent frameshift DNA synthesis by human DNA polymerase mu. Mol Cell Biol 21: 7995-8006.
-
(2001)
Mol Cell Biol
, vol.21
, pp. 7995-8006
-
-
Zhang, Y.1
Wu, X.2
Yuan, F.3
Xie, Z.4
Wang, Z.5
-
18
-
-
0347723976
-
Lesion bypass by human DNA polymerase mu reveals a template-dependent, sequence-independent nucleotidyl transferase activity
-
Covo S, Blanco L, Livneh Z, (2004) Lesion bypass by human DNA polymerase mu reveals a template-dependent, sequence-independent nucleotidyl transferase activity. J Biol Chem 279: 859-865.
-
(2004)
J Biol Chem
, vol.279
, pp. 859-865
-
-
Covo, S.1
Blanco, L.2
Livneh, Z.3
-
19
-
-
7244255742
-
Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu
-
Roettger MP, Fiala KA, Sompalli S, Dong Y, Suo Z, (2004) Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu. Biochemistry 43: 13827-13838.
-
(2004)
Biochemistry
, vol.43
, pp. 13827-13838
-
-
Roettger, M.P.1
Fiala, K.A.2
Sompalli, S.3
Dong, Y.4
Suo, Z.5
-
20
-
-
0242634246
-
DNA polymerase mu (Pol mu), homologous to TdT, could act as a DNA mutator in eukaryotic cells
-
Dominguez O, Ruiz JF, Lain de Lera T, Garcia-Diaz M, Gonzalez MA, et al. (2000) DNA polymerase mu (Pol mu), homologous to TdT, could act as a DNA mutator in eukaryotic cells. EMBO J 19: 1731-1742.
-
(2000)
EMBO J
, vol.19
, pp. 1731-1742
-
-
Dominguez, O.1
Ruiz, J.F.2
Lain de Lera, T.3
Garcia-Diaz, M.4
Gonzalez, M.A.5
-
21
-
-
0036293744
-
Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair
-
Mahajan KN, Nick McElhinny SA, Mitchell BS, Ramsden DA, (2002) Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair. Mol Cell Biol 22: 5194-5202.
-
(2002)
Mol Cell Biol
, vol.22
, pp. 5194-5202
-
-
Mahajan, K.N.1
Nick McElhinny, S.A.2
Mitchell, B.S.3
Ramsden, D.A.4
-
22
-
-
23044453811
-
A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining
-
Nick McElhinny SA, Havener JM, Garcia-Diaz M, Juarez R, Bebenek K, et al. (2005) A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. Mol Cell 19: 357-366.
-
(2005)
Mol Cell
, vol.19
, pp. 357-366
-
-
Nick McElhinny, S.A.1
Havener, J.M.2
Garcia-Diaz, M.3
Juarez, R.4
Bebenek, K.5
-
23
-
-
0041931065
-
Immunoglobulin kappa light chain gene rearrangement is impaired in mice deficient for DNA polymerase mu
-
Bertocci B, De Smet A, Berek C, Weill JC, Reynaud CA, (2003) Immunoglobulin kappa light chain gene rearrangement is impaired in mice deficient for DNA polymerase mu. Immunity 19: 203-211.
-
(2003)
Immunity
, vol.19
, pp. 203-211
-
-
Bertocci, B.1
de Smet, A.2
Berek, C.3
Weill, J.C.4
Reynaud, C.A.5
-
24
-
-
33745997776
-
Nonoverlapping functions of DNA polymerases Mu, lambda, and terminal deoxynucleotidyltransferase during immunoglobulin V(D)J recombination in vivo
-
Bertocci B, De Smet A, Weill JC, Reynaud CA, (2006) Nonoverlapping functions of DNA polymerases Mu, lambda, and terminal deoxynucleotidyltransferase during immunoglobulin V(D)J recombination in vivo. Immunity 25: 31-41.
-
(2006)
Immunity
, vol.25
, pp. 31-41
-
-
Bertocci, B.1
de Smet, A.2
Weill, J.C.3
Reynaud, C.A.4
-
25
-
-
70349499328
-
Limited terminal transferase in human DNA polymerase mu defines the required balance between accuracy and efficiency in NHEJ
-
Andrade P, Martin MJ, Juarez R, de Saro FL, Blanco L, (2009) Limited terminal transferase in human DNA polymerase mu defines the required balance between accuracy and efficiency in NHEJ. Proceedings of the National Academy of Sciences of the United States of America 106: 16203-16208.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 16203-16208
-
-
Andrade, P.1
Martin, M.J.2
Juarez, R.3
de Saro, F.L.4
Blanco, L.5
-
26
-
-
78049376599
-
Lack of DNA polymerase μ affects the kinetics of DNA double-strand break repair and impacts on cellular senescence
-
Chayot R, Danckaert A, Montagne B, Ricchetti M, (2010) Lack of DNA polymerase μ affects the kinetics of DNA double-strand break repair and impacts on cellular senescence. DNA Repair 9: 1187-1199.
-
(2010)
DNA Repair
, vol.9
, pp. 1187-1199
-
-
Chayot, R.1
Danckaert, A.2
Montagne, B.3
Ricchetti, M.4
-
27
-
-
84855339814
-
DNA polymerase μ is a global player in the repair of non-homologous end-joining substrates
-
Chayot R, Montagne B, Ricchetti M, (2012) DNA polymerase μ is a global player in the repair of non-homologous end-joining substrates. DNA Repair 11: 22-34.
-
(2012)
DNA Repair
, vol.11
, pp. 22-34
-
-
Chayot, R.1
Montagne, B.2
Ricchetti, M.3
-
28
-
-
84868679968
-
DNA polymerases in nonhomologous end joining: Are there any benefits to standing out from the crowd?
-
Ramsden DA, Asagoshi K, (2012) DNA polymerases in nonhomologous end joining: Are there any benefits to standing out from the crowd? Environmental and Molecular Mutagenesis 53: 741-751.
-
(2012)
Environmental and Molecular Mutagenesis
, vol.53
, pp. 741-751
-
-
Ramsden, D.A.1
Asagoshi, K.2
-
29
-
-
78649264729
-
Modeling DNA polymerase mu motions: subtle transitions before chemistry
-
Li Y, Schlick T, (2010) Modeling DNA polymerase mu motions: subtle transitions before chemistry. Biophysical Journal 99: 3463-3472.
-
(2010)
Biophysical Journal
, vol.99
, pp. 3463-3472
-
-
Li, Y.1
Schlick, T.2
-
30
-
-
33846075032
-
Structural insight into the substrate specificity of DNA Polymerase mu
-
Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, et al. (2007) Structural insight into the substrate specificity of DNA Polymerase mu. Nat Struct Mol Biol 14: 45-53.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 45-53
-
-
Moon, A.F.1
Garcia-Diaz, M.2
Bebenek, K.3
Davis, B.J.4
Zhong, X.5
-
31
-
-
84860729830
-
Substrate-Dependent Millisecond Domain Motions in DNA Polymerase β
-
Berlow RB, Swain M, Dalal S, Sweasy JB, Loria JP, (2012) Substrate-Dependent Millisecond Domain Motions in DNA Polymerase β. Journal of Molecular Biology 419: 171-182.
-
(2012)
Journal of Molecular Biology
, vol.419
, pp. 171-182
-
-
Berlow, R.B.1
Swain, M.2
Dalal, S.3
Sweasy, J.B.4
Loria, J.P.5
-
32
-
-
15744387367
-
Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate
-
Arora K, Schlick T, (2005) Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate. J Phys Chem B 109: 5358-5367.
-
(2005)
J Phys Chem B
, vol.109
, pp. 5358-5367
-
-
Arora, K.1
Schlick, T.2
-
33
-
-
15744396923
-
In silico evidence for DNA polymerase-beta's substrate-induced conformational change
-
Arora K, Schlick T, (2004) In silico evidence for DNA polymerase-beta's substrate-induced conformational change. Biophys J 87: 3088-3099.
-
(2004)
Biophys J
, vol.87
, pp. 3088-3099
-
-
Arora, K.1
Schlick, T.2
-
34
-
-
33646127783
-
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism
-
Sampoli Benitez BA, Arora K, Schlick T, (2006) In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism. Biophys J 90: 42-56.
-
(2006)
Biophys J
, vol.90
, pp. 42-56
-
-
Sampoli Benitez, B.A.1
Arora, K.2
Schlick, T.3
-
35
-
-
11444264188
-
A closed conformation for the Pol lambda catalytic cycle
-
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC, (2005) A closed conformation for the Pol lambda catalytic cycle. Nat Struct Mol Biol 12: 97-98.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 97-98
-
-
Garcia-Diaz, M.1
Bebenek, K.2
Krahn, J.M.3
Kunkel, T.A.4
Pedersen, L.C.5
-
36
-
-
33751207427
-
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda
-
Foley MC, Arora K, Schlick T, (2006) Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda. Biophys J 91: 3182-3195.
-
(2006)
Biophys J
, vol.91
, pp. 3182-3195
-
-
Foley, M.C.1
Arora, K.2
Schlick, T.3
-
37
-
-
43049132184
-
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda
-
Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, et al. (2008) Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda. EMBO Rep 9: 459-464.
-
(2008)
EMBO Rep
, vol.9
, pp. 459-464
-
-
Bebenek, K.1
Garcia-Diaz, M.2
Foley, M.C.3
Pedersen, L.C.4
Schlick, T.5
-
38
-
-
41149159633
-
Simulations of DNA pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin
-
Foley MC, Schlick T, (2008) Simulations of DNA pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin. J Am Chem Soc 130: 3967-3977.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 3967-3977
-
-
Foley, M.C.1
Schlick, T.2
-
39
-
-
84869433153
-
Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms
-
Schlick T, Arora K, Beard W, Wilson S, (2012) Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Theoretical Chemistry Accounts 131: 1-8.
-
(2012)
Theoretical Chemistry Accounts
, vol.131
, pp. 1-8
-
-
Schlick, T.1
Arora, K.2
Beard, W.3
Wilson, S.4
-
41
-
-
26444470895
-
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity
-
Arora K, Beard WA, Wilson SH, Schlick T, (2005) Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. Biochemistry 44: 13328-13341.
-
(2005)
Biochemistry
, vol.44
, pp. 13328-13341
-
-
Arora, K.1
Beard, W.A.2
Wilson, S.H.3
Schlick, T.4
-
42
-
-
25444442374
-
Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair
-
Radhakrishnan R, Schlick T, (2005) Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair. J Am Chem Soc 127: 13245-13252.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 13245-13252
-
-
Radhakrishnan, R.1
Schlick, T.2
-
43
-
-
0036382849
-
Local deformations revealed by dynamics simulations of DNA polymerase beta with DNA mismatches at the primer terminus
-
Yang LJ, Beard WA, Wilson SH, Roux B, Broyde S, et al. (2002) Local deformations revealed by dynamics simulations of DNA polymerase beta with DNA mismatches at the primer terminus. Journal of Molecular Biology 321: 459-478.
-
(2002)
Journal of Molecular Biology
, vol.321
, pp. 459-478
-
-
Yang, L.J.1
Beard, W.A.2
Wilson, S.H.3
Roux, B.4
Broyde, S.5
-
44
-
-
34247623128
-
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-OxoG in DNA polymerase beta
-
Wang YL, Reddy S, Beard WA, Wilson SH, Schlick T, (2007) Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-OxoG in DNA polymerase beta. Biophysical Journal 92: 3063-3070.
-
(2007)
Biophysical Journal
, vol.92
, pp. 3063-3070
-
-
Wang, Y.L.1
Reddy, S.2
Beard, W.A.3
Wilson, S.H.4
Schlick, T.5
-
45
-
-
33847781230
-
Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides
-
Wang YL, Schlick T, (2007) Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides. BMC Structural Biology 7: 7.
-
(2007)
BMC Structural Biology
, vol.7
, pp. 7
-
-
Wang, Y.L.1
Schlick, T.2
-
46
-
-
56949098651
-
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation
-
Sampoli Benitez BA, Arora K, Balistreri L, Schlick T, (2008) Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. Journal of Molecular Biology 384: 1086-1097.
-
(2008)
Journal of Molecular Biology
, vol.384
, pp. 1086-1097
-
-
Sampoli Benitez, B.A.1
Arora, K.2
Balistreri, L.3
Schlick, T.4
-
47
-
-
70349489893
-
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates
-
Foley MC, Schlick T, (2009) Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates. J Phys Chem B 113: 13035-13047.
-
(2009)
J Phys Chem B
, vol.113
, pp. 13035-13047
-
-
Foley, M.C.1
Schlick, T.2
-
48
-
-
84859412476
-
How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations
-
Kirmizialtin S, Nguyen V, Johnson Kenneth A, Elber R, (2012) How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations. Structure 20: 618-627.
-
(2012)
Structure
, vol.20
, pp. 618-627
-
-
Kirmizialtin, S.1
Nguyen, V.2
Johnson Kenneth, A.3
Elber, R.4
-
49
-
-
76249127905
-
Conformational transitions in DNA polymerase I revealed by single-molecule FRET
-
Santoso Y, Joyce CM, Potapova O, Le Reste L, Hohlbein J, et al. (2010) Conformational transitions in DNA polymerase I revealed by single-molecule FRET. Proceedings of the National Academy of Sciences of the United States of America 107: 715-720.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 715-720
-
-
Santoso, Y.1
Joyce, C.M.2
Potapova, O.3
Le Reste, L.4
Hohlbein, J.5
-
50
-
-
55549109430
-
Role of induced fit in enzyme specificity: A molecular forward/reverse switch
-
Johnson KA, (2008) Role of induced fit in enzyme specificity: A molecular forward/reverse switch. Journal of Biological Chemistry 283: 26297-26301.
-
(2008)
Journal of Biological Chemistry
, vol.283
, pp. 26297-26301
-
-
Johnson, K.A.1
-
51
-
-
84863676249
-
Watching DNA polymerase eta make a phosphodiester bond
-
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W, (2012) Watching DNA polymerase eta make a phosphodiester bond. Nature 487: 196-201.
-
(2012)
Nature
, vol.487
, pp. 196-201
-
-
Nakamura, T.1
Zhao, Y.2
Yamagata, Y.3
Hua, Y.J.4
Yang, W.5
-
52
-
-
84872530276
-
Chapter 4 Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism
-
In: Schlick T, editor
-
Foley MC, Arora K, Schlick T (2012) Chapter 4 Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism. In: Schlick T, editor. Innovations in Biomolecular Modeling and Simulations: The Royal Society of Chemistry. pp. 81-110.
-
(2012)
Innovations in Biomolecular Modeling and Simulations: The Royal Society of Chemistry
, pp. 81-110
-
-
Foley, M.C.1
Arora, K.2
Schlick, T.3
-
53
-
-
78649867646
-
Accounting for induced-fit effects in docking: what is possible and what is not?
-
Sotriffer CA, (2011) Accounting for induced-fit effects in docking: what is possible and what is not? Current Topics in Medicinal Chemistry 11: 179-191.
-
(2011)
Current Topics in Medicinal Chemistry
, vol.11
, pp. 179-191
-
-
Sotriffer, C.A.1
-
54
-
-
82455171948
-
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein
-
Bucher D, Grant BJ, McCammon JA, (2011) Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry 50: 10530-10539.
-
(2011)
Biochemistry
, vol.50
, pp. 10530-10539
-
-
Bucher, D.1
Grant, B.J.2
McCammon, J.A.3
-
55
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange OF, Lakomek NA, Fares C, Schroder GF, Walter KF, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320: 1471-1475.
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.A.2
Fares, C.3
Schroder, G.F.4
Walter, K.F.5
-
57
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE, (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology 5: 789-796.
-
(2009)
Nature Chemical Biology
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
59
-
-
79956058665
-
Biomolecular modeling and simulation: a field coming of age
-
Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X, (2011) Biomolecular modeling and simulation: a field coming of age. Quarterly Reviews of Biophysics 44: 191-228.
-
(2011)
Quarterly Reviews of Biophysics
, vol.44
, pp. 191-228
-
-
Schlick, T.1
Collepardo-Guevara, R.2
Halvorsen, L.A.3
Jung, S.4
Xiao, X.5
-
60
-
-
23444447967
-
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate
-
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH, (2005) Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Structure 13: 1225-1233.
-
(2005)
Structure
, vol.13
, pp. 1225-1233
-
-
Batra, V.K.1
Beard, W.A.2
Shock, D.D.3
Pedersen, L.C.4
Wilson, S.H.5
-
61
-
-
0029878720
-
VMD: visual molecular dynamics
-
Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. Journal of Molecular Graphics & Modelling 14: 33-38, 33-38, 27-38.
-
(1996)
Journal of Molecular Graphics & Modelling
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
62
-
-
84986512474
-
Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) Charmm- a Program for Macromolecular Energy, Minimization, and Dynamics Calculations. Journal of Computational Chemistry 4: 187-217.
-
(1983)
Journal of Computational Chemistry
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
-
63
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102: 3586-3616.
-
(1998)
Journal of Physical Chemistry B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
-
64
-
-
0000214231
-
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
-
MacKerell AD, Banavali NK, (2000) All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. Journal of Computational Chemistry 21: 105-120.
-
(2000)
Journal of Computational Chemistry
, vol.21
, pp. 105-120
-
-
MacKerell, A.D.1
Banavali, N.K.2
-
65
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell AD Jr, Feig M, Brooks CL 3rd, (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-1415.
-
(2004)
J Comput Chem
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks 3rd, C.L.3
-
66
-
-
33646940952
-
Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical-Integration of Cartesian Equations of Motion of a System with Constraints- Molecular-Dynamics of N-Alkanes. Journal of Computational Physics 23: 327-341.
-
(1977)
Journal of Computational Physics
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
67
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 26: 1781-1802.
-
(2005)
Journal of Computational Chemistry
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
-
68
-
-
36449007836
-
Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method
-
Feller SE, Zhang YH, Pastor RW, Brooks BR, (1995) Constant-Pressure Molecular-Dynamics Simulation- the Langevin Piston Method. Journal of Chemical Physics 103: 4613-4621.
-
(1995)
Journal of Chemical Physics
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
69
-
-
33846823909
-
Particle mesh Ewald: An N · log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N · log(N) method for Ewald sums in large systems. Journal of Chemical Physics 98: 10089-10092.
-
(1993)
Journal of Chemical Physics
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
70
-
-
34547842072
-
Role of the catalytic metal during polymerization by DNA polymerase lambda
-
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA, (2007) Role of the catalytic metal during polymerization by DNA polymerase lambda. DNA Repair 6: 1333-1340.
-
(2007)
DNA Repair
, vol.6
, pp. 1333-1340
-
-
Garcia-Diaz, M.1
Bebenek, K.2
Krahn, J.M.3
Pedersen, L.C.4
Kunkel, T.A.5
-
71
-
-
0031053276
-
DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant
-
Ahn J, Werneburg BG, Tsai MD, (1997) DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant. Biochemistry 36: 1100-1107.
-
(1997)
Biochemistry
, vol.36
, pp. 1100-1107
-
-
Ahn, J.1
Werneburg, B.G.2
Tsai, M.D.3
-
72
-
-
0030010766
-
DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity
-
Werneburg BG, Ahn J, Zhong X, Hondal RJ, Kraynov VS, et al. (1996) DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity. Biochemistry 35: 7041-7050.
-
(1996)
Biochemistry
, vol.35
, pp. 7041-7050
-
-
Werneburg, B.G.1
Ahn, J.2
Zhong, X.3
Hondal, R.J.4
Kraynov, V.S.5
-
73
-
-
0033597779
-
Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove
-
Osheroff WP, Beard WA, Wilson SH, Kunkel TA, (1999) Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove. J Biol Chem 274: 20749-20752.
-
(1999)
J Biol Chem
, vol.274
, pp. 20749-20752
-
-
Osheroff, W.P.1
Beard, W.A.2
Wilson, S.H.3
Kunkel, T.A.4
-
77
-
-
0033105094
-
Conserved domains in DNA repair proteins and evolution of repair systems
-
Aravind L, Walker DR, Koonin EV, (1999) Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Research 27: 1223-1242.
-
(1999)
Nucleic Acids Research
, vol.27
, pp. 1223-1242
-
-
Aravind, L.1
Walker, D.R.2
Koonin, E.V.3
|