-
1
-
-
13244279669
-
Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain
-
Nagadoi A, Morikawa S, Nakamura H, Enari M, Kobayashi K, et al. (1995) Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain. Structure 3: 1217-1224.
-
(1995)
Structure
, vol.3
, pp. 1217-1224
-
-
Nagadoi, A.1
Morikawa, S.2
Nakamura, H.3
Enari, M.4
Kobayashi, K.5
-
2
-
-
0025009802
-
Protein DNA Conformational-Changes in the Crystal-Structure of a Lambda-Cro-Operator Complex
-
Brennan RG, Roderick SL, Takeda Y, Matthews BW, (1990) Protein DNA Conformational-Changes in the Crystal-Structure of a Lambda-Cro-Operator Complex. Proc Natl Acad Sci U S A 87: 8165-8169.
-
(1990)
Proc Natl Acad Sci U S A
, vol.87
, pp. 8165-8169
-
-
Brennan, R.G.1
Roderick, S.L.2
Takeda, Y.3
Matthews, B.W.4
-
3
-
-
0034697977
-
Conformational changes and cleavage by the homing endonuclease I-Ppol: A critical role for a leucine residue in the active site
-
Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, et al. (2000) Conformational changes and cleavage by the homing endonuclease I-Ppol: A critical role for a leucine residue in the active site. J Mol Biol 300: 877-887.
-
(2000)
J Mol Biol
, vol.300
, pp. 877-887
-
-
Galburt, E.A.1
Chadsey, M.S.2
Jurica, M.S.3
Chevalier, B.S.4
Erho, D.5
-
4
-
-
0032489427
-
Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein
-
Hegde RS, Wang AF, Kim SS, Schapira M, (1998) Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein. J Mol Biol 276: 797-808.
-
(1998)
J Mol Biol
, vol.276
, pp. 797-808
-
-
Hegde, R.S.1
Wang, A.F.2
Kim, S.S.3
Schapira, M.4
-
5
-
-
0032509980
-
Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex
-
Tan S, Richmond TJ, (1998) Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391: 660-666.
-
(1998)
Nature
, vol.391
, pp. 660-666
-
-
Tan, S.1
Richmond, T.J.2
-
6
-
-
0032545160
-
Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism
-
Hegde RS, Androphy EJ, (1998) Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism. J Mol Biol 284: 1479-1489.
-
(1998)
J Mol Biol
, vol.284
, pp. 1479-1489
-
-
Hegde, R.S.1
Androphy, E.J.2
-
7
-
-
34247393616
-
Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation
-
Falconi M, Santolamazza A, Eliseo T, de Prat-Gay G, Cicero DO, et al. (2007) Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation. Febs J 274: 2385-2395.
-
(2007)
Febs J
, vol.274
, pp. 2385-2395
-
-
Falconi, M.1
Santolamazza, A.2
Eliseo, T.3
de Prat-Gay, G.4
Cicero, D.O.5
-
8
-
-
51049122626
-
MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation
-
Falconi M, Oteri F, Eliseo T, Cicero DO, Desideri A, (2008) MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation. Biophys J 95: 1108-1117.
-
(2008)
Biophys J
, vol.95
, pp. 1108-1117
-
-
Falconi, M.1
Oteri, F.2
Eliseo, T.3
Cicero, D.O.4
Desideri, A.5
-
9
-
-
0024052649
-
Flexibility of the yeast alpha 2 repressor enables it to occupy the ends of its operator, leaving the center free
-
Sauer RT, Smith DL, Johnson AD, (1988) Flexibility of the yeast alpha 2 repressor enables it to occupy the ends of its operator, leaving the center free. Genes Dev 2: 807-816.
-
(1988)
Genes Dev
, vol.2
, pp. 807-816
-
-
Sauer, R.T.1
Smith, D.L.2
Johnson, A.D.3
-
10
-
-
0027509952
-
A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein
-
Vershon AK, Johnson AD, (1993) A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein. Cell 72: 105-112.
-
(1993)
Cell
, vol.72
, pp. 105-112
-
-
Vershon, A.K.1
Johnson, A.D.2
-
11
-
-
0035022941
-
Intrinsically disordered protein
-
Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, et al. (2001) Intrinsically disordered protein. J Mol Graph Model 19: 26-59.
-
(2001)
J Mol Graph Model
, vol.19
, pp. 26-59
-
-
Dunker, A.K.1
Lawson, J.D.2
Brown, C.J.3
Williams, R.M.4
Romero, P.5
-
12
-
-
0036803243
-
Intrinsically unstructured proteins
-
Tompa P, (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27: 527-533.
-
(2002)
Trends Biochem Sci
, vol.27
, pp. 527-533
-
-
Tompa, P.1
-
13
-
-
33744961763
-
Intrinsic disorder in transcription factors
-
Liu J, Perumal NB, Oldfield CJ, Su EW, Uversky VN, et al. (2006) Intrinsic disorder in transcription factors. Biochemistry 45: 6873-6888.
-
(2006)
Biochemistry
, vol.45
, pp. 6873-6888
-
-
Liu, J.1
Perumal, N.B.2
Oldfield, C.J.3
Su, E.W.4
Uversky, V.N.5
-
14
-
-
33744829805
-
Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation
-
Minezaki Y, Homma K, Kinjo AR, Nishikawa K, (2006) Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J Mol Biol 359: 1137-1149.
-
(2006)
J Mol Biol
, vol.359
, pp. 1137-1149
-
-
Minezaki, Y.1
Homma, K.2
Kinjo, A.R.3
Nishikawa, K.4
-
15
-
-
82655175469
-
Roles of intrinsic disorder in protein-nucleic acid interactions
-
Dyson HJ, (2012) Roles of intrinsic disorder in protein-nucleic acid interactions. Mol Biosyst 8: 97-104.
-
(2012)
Mol Biosyst
, vol.8
, pp. 97-104
-
-
Dyson, H.J.1
-
16
-
-
76549252207
-
The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain
-
Pauling L, Corey RB, Branson HR, (1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 37: 205-211.
-
(1951)
Proc Natl Acad Sci U S A
, vol.37
, pp. 205-211
-
-
Pauling, L.1
Corey, R.B.2
Branson, H.R.3
-
17
-
-
77449117443
-
Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins
-
Dan A, Ofran Y, Kliger Y, (2009) Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins. Proteins 78: 236-248.
-
(2009)
Proteins
, vol.78
, pp. 236-248
-
-
Dan, A.1
Ofran, Y.2
Kliger, Y.3
-
18
-
-
0031871068
-
Chameleon sequences in the PDB
-
Mezei M, (1998) Chameleon sequences in the PDB. Protein Eng 11: 411-414.
-
(1998)
Protein Eng
, vol.11
, pp. 411-414
-
-
Mezei, M.1
-
19
-
-
41149162869
-
Local Protein Structures Current Bioinformatics
-
Offmann B, Tyagi M, de Brevern AG, (2007) Local Protein Structures Current Bioinformatics. 2: 165-202.
-
(2007)
, vol.2
, pp. 165-202
-
-
Offmann, B.1
Tyagi, M.2
de Brevern, A.G.3
-
20
-
-
61649097231
-
Structural alphabets for protein structure classification: a comparison study
-
Le Q, Pollastri G, Koehl P, (2009) Structural alphabets for protein structure classification: a comparison study. J Mol Biol 387: 431-450.
-
(2009)
J Mol Biol
, vol.387
, pp. 431-450
-
-
Le, Q.1
Pollastri, G.2
Koehl, P.3
-
21
-
-
66249111103
-
Enhanced protein fold recognition using a structural alphabet
-
Deschavanne P, Tuffery P, (2009) Enhanced protein fold recognition using a structural alphabet. Proteins 76: 129-137.
-
(2009)
Proteins
, vol.76
, pp. 129-137
-
-
Deschavanne, P.1
Tuffery, P.2
-
22
-
-
0034669774
-
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
-
de Brevern AG, Etchebest C, Hazout S, (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 41: 271-287.
-
(2000)
Proteins
, vol.41
, pp. 271-287
-
-
de Brevern, A.G.1
Etchebest, C.2
Hazout, S.3
-
23
-
-
18844454820
-
A structural alphabet for local protein structures: improved prediction methods
-
Etchebest C, Benros C, Hazout S, de Brevern AG, (2005) A structural alphabet for local protein structures: improved prediction methods. Proteins 59: 810-827.
-
(2005)
Proteins
, vol.59
, pp. 810-827
-
-
Etchebest, C.1
Benros, C.2
Hazout, S.3
de Brevern, A.G.4
-
24
-
-
33846653633
-
Using an alignment of fragment strings for comparing protein structures
-
Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, et al. (2007) Using an alignment of fragment strings for comparing protein structures. Bioinformatics 23: e219-224.
-
(2007)
Bioinformatics
, vol.23
-
-
Friedberg, I.1
Harder, T.2
Kolodny, R.3
Sitbon, E.4
Li, Z.5
-
25
-
-
34250167965
-
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
-
Tung CH, Huang JW, Yang JM, (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol 8: R31.
-
(2007)
Genome Biol
, vol.8
-
-
Tung, C.H.1
Huang, J.W.2
Yang, J.M.3
-
26
-
-
34147202792
-
Discovering structural motifs using a structural alphabet: application to magnesium-binding sites
-
Dudev M, Lim C, (2007) Discovering structural motifs using a structural alphabet: application to magnesium-binding sites. BMC Bioinformatics 8: 106.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 106
-
-
Dudev, M.1
Lim, C.2
-
27
-
-
42449108256
-
Structural deformation upon protein-protein interaction: a structural alphabet approach
-
Martin J, Regad L, Lecornet H, Camproux AC, (2008) Structural deformation upon protein-protein interaction: a structural alphabet approach. BMC Struct Biol 8: 12.
-
(2008)
BMC Struct Biol
, vol.8
, pp. 12
-
-
Martin, J.1
Regad, L.2
Lecornet, H.3
Camproux, A.C.4
-
28
-
-
79351469310
-
Deciphering the shape and deformation of secondary structures through local conformation analysis
-
Baussand J, Camproux AC, (2011) Deciphering the shape and deformation of secondary structures through local conformation analysis. BMC Struct Biol 11: 9.
-
(2011)
BMC Struct Biol
, vol.11
, pp. 9
-
-
Baussand, J.1
Camproux, A.C.2
-
29
-
-
77950469105
-
De novo backbone scaffolds for protein design
-
MacDonald JT, Maksimiak K, Sadowski MI, Taylor WR, (2009) De novo backbone scaffolds for protein design. Proteins 78: 1311-1325.
-
(2009)
Proteins
, vol.78
, pp. 1311-1325
-
-
MacDonald, J.T.1
Maksimiak, K.2
Sadowski, M.I.3
Taylor, W.R.4
-
30
-
-
0036406112
-
Small libraries of protein fragments model native protein structures accurately
-
Kolodny R, Koehl P, Guibas L, Levitt M, (2002) Small libraries of protein fragments model native protein structures accurately. J Mol Biol 323: 297-307.
-
(2002)
J Mol Biol
, vol.323
, pp. 297-307
-
-
Kolodny, R.1
Koehl, P.2
Guibas, L.3
Levitt, M.4
-
31
-
-
0042622240
-
GlobPlot: Exploring protein sequences for globularity and disorder
-
Linding R, Russell RB, Neduva V, Gibson TJ, (2003) GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 31: 3701-3708.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3701-3708
-
-
Linding, R.1
Russell, R.B.2
Neduva, V.3
Gibson, T.J.4
-
32
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
33
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
34
-
-
84913591509
-
Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency
-
Eisenhaber F, Argos P, (1993) Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency. Journal of Computational Chemistry 14: 1272-1280.
-
(1993)
Journal of Computational Chemistry
, vol.14
, pp. 1272-1280
-
-
Eisenhaber, F.1
Argos, P.2
-
36
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
37
-
-
33745757784
-
Molecular flexibility in protein-DNA interactions
-
Gunther S, Rother K, Frommel C, (2006) Molecular flexibility in protein-DNA interactions. Biosystems 85: 126-136.
-
(2006)
Biosystems
, vol.85
, pp. 126-136
-
-
Gunther, S.1
Rother, K.2
Frommel, C.3
-
38
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
Jones S, van Heyningen P, Berman HM, Thornton JM, (1999) Protein-DNA interactions: A structural analysis. J Mol Biol 287: 877-896.
-
(1999)
J Mol Biol
, vol.287
, pp. 877-896
-
-
Jones, S.1
van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
39
-
-
26444598454
-
Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure
-
Lejeune D, Delsaux N, Charloteaux B, Thomas A, Brasseur R, (2005) Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. Proteins 61: 258-271.
-
(2005)
Proteins
, vol.61
, pp. 258-271
-
-
Lejeune, D.1
Delsaux, N.2
Charloteaux, B.3
Thomas, A.4
Brasseur, R.5
-
40
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
Nadassy K, Wodak SJ, Janin J, (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry 38: 1999-2017.
-
(1999)
Biochemistry
, vol.38
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
41
-
-
69049084284
-
Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes
-
Biswas S, Guharoy M, Chakrabarti P, (2008) Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes. Bioinformation 2: 422-427.
-
(2008)
Bioinformation
, vol.2
, pp. 422-427
-
-
Biswas, S.1
Guharoy, M.2
Chakrabarti, P.3
|