-
1
-
-
0036017388
-
Evolutionary rate heterogeneity in proteins with long disordered regions
-
DOI 10.1007/s00239-001-2309-6
-
Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, et al. (2002) Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 55: 104-110. (Pubitemid 34634364)
-
(2002)
Journal of Molecular Evolution
, vol.55
, Issue.1
, pp. 104-110
-
-
Brown, C.J.1
Takayama, S.2
Campen, A.M.3
Vise, P.4
Marshall, T.W.5
Oldfield, C.J.6
Williams, C.J.7
Keith, D.A.8
-
2
-
-
63749116038
-
Allostery in the LacI/GalR family: Variations on a theme
-
Swint-Kruse L, Matthews KS (2009) Allostery in the LacI/GalR family: variations on a theme. Curr Opin Microbiol 12: 129-137.
-
(2009)
Curr Opin Microbiol
, vol.12
, pp. 129-137
-
-
Swint-Kruse, L.1
Matthews, K.S.2
-
3
-
-
33846516797
-
The lactose repressor system: Paradigms for regulation, allosteric behavior and protein folding
-
DOI 10.1007/s00018-006-6296-z
-
Wilson CJ, Zhan H, Swint-Kruse L, Matthews KS (2007) The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding. Cell Mol Life Sci 64: 3-16. (Pubitemid 46164491)
-
(2007)
Cellular and Molecular Life Sciences
, vol.64
, Issue.1
, pp. 3-16
-
-
Wilson, C.J.1
Zhan, H.2
Swint-Kruse, L.3
Matthews, K.S.4
-
4
-
-
84870607623
-
Novel insights from hybrid LacI/GalR proteins: Family-wide functional attributes and biologically significant variation in transcription repression
-
Meinhardt S, Manley MW Jr, Becker NA, Hessman JA, Maher LJ III, et al. (2012) Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression. Nucleic Acids Res 40: 11139-11154.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11139-11154
-
-
Meinhardt, S.1
Manley Jr., M.W.2
Becker, N.A.3
Hessman, J.A.4
Maher III, L.J.5
-
5
-
-
58149292217
-
Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: Bioinformaticsbased predictions generate true positives and false negatives
-
Meinhardt S, Swint-Kruse L (2008) Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformaticsbased predictions generate true positives and false negatives. Proteins 73: 941-957.
-
(2008)
Proteins
, vol.73
, pp. 941-957
-
-
Meinhardt, S.1
Swint-Kruse, L.2
-
6
-
-
73849085331
-
Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: Implications for sequence/function analyses
-
Tungtur S, Meinhardt S, Swint-Kruse L (2010) Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J Mol Biol 395: 785-802.
-
(2010)
J Mol Biol
, vol.395
, pp. 785-802
-
-
Tungtur, S.1
Meinhardt, S.2
Swint-Kruse, L.3
-
7
-
-
3442888250
-
Bayesian approach to discovering pathogenic SNPs in conserved protein domains
-
DOI 10.1002/humu.20063
-
Cai Z, Tsung EF, Marinescu VD, Ramoni MF, Riva A, et al. (2004) Bayesian approach to discovering pathogenic SNPs in conserved protein domains. Hum Mutat 24: 178-184. (Pubitemid 39006598)
-
(2004)
Human Mutation
, vol.24
, Issue.2
, pp. 178-184
-
-
Cai, Z.1
Tsung, E.F.2
Marinescu, V.D.3
Ramoni, M.F.4
Riva, A.5
Kohane, I.S.6
-
8
-
-
33750578872
-
Searching for interpretable rules for disease mutations: A simulated annealing bump hunting strategy
-
Jiang R, Yang H, Sun F, Chen T (2006) Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinformatics 7: 417.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 417
-
-
Jiang, R.1
Yang, H.2
Sun, F.3
Chen, T.4
-
9
-
-
1642452921
-
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families
-
DOI 10.1110/ps.03191704
-
Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB (2004) Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci 13: 443-456. (Pubitemid 38124965)
-
(2004)
Protein Science
, vol.13
, Issue.2
, pp. 443-456
-
-
Kalinina, O.V.1
Mironov, A.A.2
Gelfand, M.S.3
Rakhmaninova, A.B.4
-
10
-
-
0344033683
-
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
-
DOI 10.1093/bioinformatics/btg297
-
Krishnan VG, Westhead DR (2003) A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 19: 2199-2209. (Pubitemid 37483977)
-
(2003)
Bioinformatics
, vol.19
, Issue.17
, pp. 2199-2209
-
-
Krishnan, V.G.1
Westhead, D.R.2
-
11
-
-
77949537825
-
Bi-directional SIFT predicts a subset of activating mutations
-
Lee W, Zhang Y, Mukhyala K, Lazarus RA, Zhang Z (2009) Bi-directional SIFT predicts a subset of activating mutations. PLoS One 4: e8311.
-
(2009)
PLoS One
, vol.4
-
-
Lee, W.1
Zhang, Y.2
Mukhyala, K.3
Lazarus, R.A.4
Zhang, Z.5
-
12
-
-
33749430068
-
Predicting the effect of missense mutations on protein function: Analysis with Bayesian networks
-
Needham CJ, Bradford JR, Bulpitt AJ, Care MA, Westhead DR (2006) Predicting the effect of missense mutations on protein function: analysis with Bayesian networks. BMC Bioinformatics 7: 405.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 405
-
-
Needham, C.J.1
Bradford, J.R.2
Bulpitt, A.J.3
Care, M.A.4
Westhead, D.R.5
-
13
-
-
0035026704
-
Predicting deleterious amino acid substitutions
-
DOI 10.1101/gr.176601
-
Ng PC, Henikoff S (2001) Predicting deleterious amino acid substitutions. Genome Res 11: 863-874. (Pubitemid 32447869)
-
(2001)
Genome Research
, vol.11
, Issue.5
, pp. 863-874
-
-
Ng, P.C.1
Henikoff, S.2
-
14
-
-
79954573471
-
Functionally important positions can comprise the majority of a protein's architecture
-
Tungtur S, Parente DJ, Swint-Kruse L (2011) Functionally important positions can comprise the majority of a protein's architecture. Proteins 79: 1589-1608.
-
(2011)
Proteins
, vol.79
, pp. 1589-1608
-
-
Tungtur, S.1
Parente, D.J.2
Swint-Kruse, L.3
-
15
-
-
41349115302
-
Tracing evolutionary pressure
-
DOI 10.1093/bioinformatics/btn057
-
Ye K, Vriend G, AP IJ (2008) Tracing evolutionary pressure. Bioinformatics 24: 908-915. (Pubitemid 351448024)
-
(2008)
Bioinformatics
, vol.24
, Issue.7
, pp. 908-915
-
-
Ye, K.1
Vriend, G.2
Ijzerman, A.P.3
-
16
-
-
0026724966
-
A family of bacterial regulators homologous to Gal and Lac repressors
-
Weickert MJ, Adhya S (1992) A family of bacterial regulators homologous to Gal and Lac repressors. J Biol Chem 267: 15869-15874.
-
(1992)
J Biol Chem
, vol.267
, pp. 15869-15874
-
-
Weickert, M.J.1
Adhya, S.2
-
17
-
-
0026682712
-
Isorepressor of the gal regulon in Escherichia coli
-
Weickert MJ, Adhya S (1992) Isorepressor of the gal regulon in Escherichia coli. J Mol Biol 226: 69-83.
-
(1992)
J Mol Biol
, vol.226
, pp. 69-83
-
-
Weickert, M.J.1
Adhya, S.2
-
18
-
-
0034089394
-
A closer view of the conformation of the Lac repressor bound to operator
-
DOI 10.1038/73317
-
Bell CE, Lewis M (2000) A closer view of the conformation of the Lac repressor bound to operator. Nat Struct Biol 7: 209-214. (Pubitemid 30140766)
-
(2000)
Nature Structural Biology
, vol.7
, Issue.3
, pp. 209-214
-
-
Bell, C.E.1
Lewis, M.2
-
19
-
-
0031677841
-
Crystal structure of the effector-binding domain of the trehalose- repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose
-
Hars U, Horlacher R, Boos W, Welte W, Diederichs K (1998) Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose. Protein Sci 7: 2511-2521. (Pubitemid 28565692)
-
(1998)
Protein Science
, vol.7
, Issue.12
, pp. 2511-2521
-
-
Hars, U.1
Horlacher, R.2
Boos, W.3
Welte, W.4
Diederichs, K.5
-
20
-
-
4544356004
-
Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P
-
DOI 10.1016/j.cell.2004.08.027, PII S0092867404007925
-
Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W, et al. (2004) Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. Cell 118: 731-741. (Pubitemid 39221732)
-
(2004)
Cell
, vol.118
, Issue.6
, pp. 731-741
-
-
Schumacher, M.A.1
Allen, G.S.2
Diel, M.3
Seidel, G.4
Hillen, W.5
Brennan, R.G.6
-
21
-
-
0030967745
-
The x-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water- mediated hydrogen bond to corepressor specificity and binding affinity
-
DOI 10.1074/jbc.272.36.22648
-
Schumacher MA, Glasfeld A, Zalkin H, Brennan RG (1997) The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity. J Biol Chem 272: 22648-22653. (Pubitemid 27386080)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.36
, pp. 22648-22653
-
-
Schumacher, M.A.1
Glasfeld, A.2
Zalkin, H.3
Brennan, R.G.4
-
24
-
-
84896705487
-
-
Bonanno JB, Freeman J, Bain KT, Iizuka M, Ozyurt S, et al. (2008) PDB 3e3m: Crystal structure of a LacI family transcriptional regulator from Silicibacter pomeroyi.
-
(2008)
PDB 3e3m: Crystal Structure of a LacI Family Transcriptional Regulator from Silicibacter Pomeroyi
-
-
Bonanno, J.B.1
Freeman, J.2
Bain, K.T.3
Iizuka, M.4
Ozyurt, S.5
-
25
-
-
84896720582
-
-
Bonanno JB, Freeman J, Bain KT, Mendoza M, Ozyurt S, et al. (2007) PDB 3bil: Crystal structure of a probable LacI family transcriptional regulator from Corynebacterium glutamicum.
-
(2007)
PDB 3bil: Crystal Structure of a Probable LacI Family Transcriptional Regulator from Corynebacterium Glutamicum
-
-
Bonanno, J.B.1
Freeman, J.2
Bain, K.T.3
Mendoza, M.4
Ozyurt, S.5
-
26
-
-
84896704701
-
-
Malashkevich VN, Toro R, Morano C, Sauder JM, Burley SK, et al. (2009) PDB 3k4h: Crystal structure of putative transcriptional regulator LacI from Bacillus cereus subsp. cytotoxis NVH 391-98.
-
(2009)
PDB 3k4h: Crystal Structure of Putative Transcriptional Regulator LacI from Bacillus Cereus Subsp. Cytotoxis NVH 391-98
-
-
Malashkevich, V.N.1
Toro, R.2
Morano, C.3
Sauder, J.M.4
Burley, S.K.5
-
29
-
-
84896728117
-
-
Patskovsky Y, Ramagopal U, Toro R, Foti R, Freeman J, et al. (2009) PDB 3jvd: Crystal structure of putative transcription regulation repressor (LacI family) from Corynebacterium glutamicum.
-
(2009)
PDB 3jvd: Crystal Structure of Putative Transcription Regulation Repressor (LacI Family) from Corynebacterium Glutamicum
-
-
Patskovsky, Y.1
Ramagopal, U.2
Toro, R.3
Foti, R.4
Freeman, J.5
-
33
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
-
34
-
-
0028137190
-
Mutagenesis of amino acid residues required for binding of corepressors to the purine repressor
-
Choi KY, Lu F, Zalkin H (1994) Mutagenesis of amino acid residues required for binding of corepressors to the purine repressor. J Biol Chem 269: 24066-24072. (Pubitemid 24300940)
-
(1994)
Journal of Biological Chemistry
, vol.269
, Issue.39
, pp. 24066-24072
-
-
Choi, K.Y.1
Lu, F.2
Zalkin, H.3
-
35
-
-
0031961672
-
Lactose repressor protein: Functional properties and structure
-
Matthews KS, Nichols JC (1998) Lactose repressor protein: functional properties and structure. Prog Nucleic Acid Res Mol Biol 58: 127-164.
-
(1998)
Prog Nucleic Acid Res Mol Biol
, vol.58
, pp. 127-164
-
-
Matthews, K.S.1
Nichols, J.C.2
-
36
-
-
0033565546
-
Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes
-
DOI 10.1093/nar/27.14.2981
-
Mironov AA, Koonin EV, Roytberg MA, Gelfand MS (1999) Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res 27: 2981-2989. (Pubitemid 29335721)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.14
, pp. 2981-2989
-
-
Mironov, A.A.1
Koonin, E.V.2
Roytberg, M.A.3
Gelfand, M.S.4
-
37
-
-
0015527295
-
lac Repressor-operator interaction. VI. The natural inducer of the lac operon
-
Jobe A, Bourgeois S (1972) lac Repressor-operator interaction. VI. The natural inducer of the lac operon. J Mol Biol 69: 397-408.
-
(1972)
J Mol Biol
, vol.69
, pp. 397-408
-
-
Jobe, A.1
Bourgeois, S.2
-
38
-
-
0026665031
-
Structural characterization and corepressor binding of the Escherichia coli purine repressor
-
Choi KY, Zalkin H (1992) Structural characterization and corepressor binding of the Escherichia coli purine repressor. J Bacteriol 174: 6207-6214.
-
(1992)
J Bacteriol
, vol.174
, pp. 6207-6214
-
-
Choi, K.Y.1
Zalkin, H.2
-
39
-
-
0025647125
-
Identification of hypoxanthine and guanine as the corepressors for the purine regulon genes of Escherichia coli
-
Meng LM, Nygaard P (1990) Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli. Mol Microbiol 4: 2187-2192. (Pubitemid 120005279)
-
(1990)
Molecular Microbiology
, vol.4
, Issue.12
, pp. 2187-2192
-
-
Meng, L.M.1
Nygaard, P.2
-
40
-
-
0037329109
-
Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins
-
DOI 10.1093/molbev/msg038
-
Fukami-Kobayashi K, Tateno Y, Nishikawa K (2003) Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins. Mol Biol Evol 20: 267-277. (Pubitemid 36237385)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.2
, pp. 267-277
-
-
Fukami-Kobayashi, K.1
Tateno, Y.2
Nishikawa, K.3
-
41
-
-
38849115223
-
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
-
DOI 10.1093/bioinformatics/btm604
-
Dunn SD, Wahl LM, Gloor GB (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24: 333-340. (Pubitemid 351189008)
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 333-340
-
-
Dunn, S.D.1
Wahl, L.M.2
Gloor, G.B.3
-
42
-
-
68749107059
-
Protein sectors: Evolutionary units of three-dimensional structure
-
Halabi N, Rivoire O, Leibler S, Ranganathan R (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell 138: 774-786.
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
43
-
-
3543089710
-
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
-
DOI 10.1093/bioinformatics/bth128
-
Dekker JP, Fodor A, Aldrich RW, Yellen G (2004) A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics 20: 1565-1572. (Pubitemid 39023160)
-
(2004)
Bioinformatics
, vol.20
, Issue.10
, pp. 1565-1572
-
-
Dekker, J.P.1
Fodor, A.2
Aldrich, R.W.3
Gary, Y.4
-
44
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel U, Sander C, Schneider R, Valencia A (1994) Correlated mutations and residue contacts in proteins. Proteins 18: 309-317. (Pubitemid 24111530)
-
(1994)
Proteins: Structure, Function and Genetics
, vol.18
, Issue.4
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
46
-
-
38049186804
-
Correlated substitution analysis and the prediction of amino acid structural contacts
-
Horner DS, Pirovano W, Pesole G (2008) Correlated substitution analysis and the prediction of amino acid structural contacts. Brief Bioinform 9: 46-56.
-
(2008)
Brief Bioinform
, vol.9
, pp. 46-56
-
-
Horner, D.S.1
Pirovano, W.2
Pesole, G.3
-
47
-
-
0036721218
-
Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
-
DOI 10.1002/prot.10180
-
Kass I, Horovitz A (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48: 611-617. (Pubitemid 34925449)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.48
, Issue.4
, pp. 611-617
-
-
Kass, I.1
Horovitz, A.2
-
48
-
-
44649153450
-
Rewiring the Specificity of Two-Component Signal Transduction Systems
-
DOI 10.1016/j.cell.2008.04.040, PII S0092867408006144
-
Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, et al. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133: 1043-1054. (Pubitemid 351787742)
-
(2008)
Cell
, vol.133
, Issue.6
, pp. 1043-1054
-
-
Skerker, J.M.1
Perchuk, B.S.2
Siryaporn, A.3
Lubin, E.A.4
Ashenberg, O.5
Goulian, M.6
Laub, M.T.7
-
49
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
DOI 10.1038/nsb881
-
Suel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10: 59-69. (Pubitemid 36034178)
-
(2003)
Nature Structural Biology
, vol.10
, Issue.1
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
50
-
-
84862027773
-
A coevolutionary residue network at the site of a functionally important conformational change in a phosphohexomutase enzyme family
-
Lee Y, Mick J, Furdui C, Beamer LJ (2012) A coevolutionary residue network at the site of a functionally important conformational change in a phosphohexomutase enzyme family. PLoS One 7: e38114.
-
(2012)
PLoS One
, vol.7
-
-
Lee, Y.1
Mick, J.2
Furdui, C.3
Beamer, L.J.4
-
51
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
DOI 10.1126/science.286.5438.295
-
Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299. (Pubitemid 29484693)
-
(1999)
Science
, vol.286
, Issue.5438
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
52
-
-
2442498470
-
On Evolutionary Conservation of Thermodynamic Coupling in Proteins
-
DOI 10.1074/jbc.M402560200
-
Fodor AA, Aldrich RW (2004) On evolutionary conservation of thermodynamic coupling in proteins. J Biol Chem 279: 19046-19050. (Pubitemid 38623335)
-
(2004)
Journal of Biological Chemistry
, vol.279
, Issue.18
, pp. 19046-19050
-
-
Fodor, A.A.1
Aldrich, R.W.2
-
53
-
-
77956219920
-
Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my!
-
Brown CA, Brown KS (2010) Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my! PLoS One 5: e10779.
-
(2010)
PLoS One
, vol.5
-
-
Brown, C.A.1
Brown, K.S.2
-
54
-
-
3042842115
-
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
-
DOI 10.1002/prot.20098
-
Fodor AA, Aldrich RW (2004) Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 56: 211-221. (Pubitemid 38850156)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.2
, pp. 211-221
-
-
Fodor, A.A.1
Aldrich, R.W.2
-
55
-
-
0033550256
-
Effective use of sequence correlation and conservation in fold recognition
-
Olmea O, Rost B, Valencia A (1999) Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 293: 1221-1239.
-
(1999)
J Mol Biol
, vol.293
, pp. 1221-1239
-
-
Olmea, O.1
Rost, B.2
Valencia, A.3
-
56
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea O, Valencia A (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des 2: S25-32. (Pubitemid 127740476)
-
(1997)
Folding and Design
, vol.2
, Issue.3
-
-
Olmea, O.1
Valencia, A.2
-
57
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
58
-
-
0036205440
-
DIVERGE: Phylogeny-based analysis for functional-structural divergence of a protein family
-
Gu X, Vander Velden K (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18: 500-501. (Pubitemid 34284959)
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 500-501
-
-
Gu, X.1
Velden, K.V.2
-
59
-
-
80052626839
-
Determinants, discriminants, conserved residues-a heuristic approach to detection of functional divergence in protein families
-
Bharatham K, Zhang ZH, Mihalek I (2011) Determinants, discriminants, conserved residues-a heuristic approach to detection of functional divergence in protein families. PLoS One 6: e24382.
-
(2011)
PLoS One
, vol.6
-
-
Bharatham, K.1
Zhang, Z.H.2
Mihalek, I.3
-
60
-
-
0036134757
-
Heterotachy, an important process of protein evolution
-
Lopez P, Casane D, Philippe H (2002) Heterotachy, an important process of protein evolution. Mol Biol Evol 19: 1-7. (Pubitemid 34008041)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.1
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
61
-
-
0032728408
-
Statistical methods for testing functional divergence after gene duplication
-
Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16: 1664-1674.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1664-1674
-
-
Gu, X.1
-
62
-
-
0031738688
-
Identification of a co-repressor binding site in catabolite control protein CcpA
-
DOI 10.1046/j.1365-2958.1998.01123.x
-
Kraus A, Kuster E, Wagner A, Hoffmann K, Hillen W (1998) Identification of a co-repressor binding site in catabolite control protein CcpA. Mol Microbiol 30: 955-963. (Pubitemid 28550120)
-
(1998)
Molecular Microbiology
, vol.30
, Issue.5
, pp. 955-963
-
-
Kraus, A.1
Kuster, E.2
Wagner, A.3
Hoffmann, K.4
Hillen, W.5
-
63
-
-
0037031862
-
Genetic analysis of GalR tetramerization in DNA looping during repressosome assembly
-
DOI 10.1074/jbc.M202445200
-
Geanacopoulos M, Adhya S (2002) Genetic analysis of GalR tetramerization in DNA looping during repressosome assembly. J Biol Chem 277: 33148-33152. (Pubitemid 34984832)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.36
, pp. 33148-33152
-
-
Geanacopoulos, M.1
Adhya, S.2
-
64
-
-
0033563076
-
GalR mutants defective in repressosome formation
-
Geanacopoulos M, Vasmatzis G, Lewis DE, Roy S, Lee B, et al. (1999) GalR mutants defective in repressosome formation. Genes Dev 13: 1251-1262. (Pubitemid 29250193)
-
(1999)
Genes and Development
, vol.13
, Issue.10
, pp. 1251-1262
-
-
Geanacopoulos, M.1
Vasmatzis, G.2
Lewis, D.E.A.3
Roy, S.4
Lee, B.5
Adhya, S.6
-
65
-
-
0001368373
-
Étude comparative de la distribution florale dans une portion des Alpes et du Jura
-
Jaccard P (1901) Étude comparative de la distribution florale dans une portion des Alpes et du Jura. Bulletin del la Société Vaudoise des Sciences Naturelles 37: 547-579.
-
(1901)
Bulletin del la Société Vaudoise des Sciences Naturelles
, vol.37
, pp. 547-579
-
-
Jaccard, P.1
-
66
-
-
84879630282
-
Environmental dependence of genetic constraint
-
de Vos MG, Poelwijk FJ, Battich N, Ndika JD, Tans SJ (2013) Environmental dependence of genetic constraint. PLoS Genet 9: e1003580.
-
(2013)
PLoS Genet
, vol.9
-
-
De Vos, M.G.1
Poelwijk, F.J.2
Battich, N.3
Ndika, J.D.4
Tans, S.J.5
-
67
-
-
0142179045
-
Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimer
-
DOI 10.1110/ps.03188303
-
Flynn TC, Swint-Kruse L, Kong Y, Booth C, Matthews KS, et al. (2003) Allosteric transition pathways in the lactose repressor protein core domains: asymmetric motions in a homodimer. Protein Sci 12: 2523-2541. (Pubitemid 37310792)
-
(2003)
Protein Science
, vol.12
, Issue.11
, pp. 2523-2541
-
-
Flynn, T.C.1
Swint-Kruse, L.2
Kong, Y.3
Booth, C.4
Matthews, K.S.5
Ma, J.6
-
68
-
-
84863969022
-
Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli
-
Qian Z, Dimitriadis EK, Edgar R, Eswaramoorthy P, Adhya S (2012) Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli. Proc Natl Acad Sci U S A 109: 11336-11341.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 11336-11341
-
-
Qian, Z.1
Dimitriadis, E.K.2
Edgar, R.3
Eswaramoorthy, P.4
Adhya, S.5
-
69
-
-
33751381461
-
TimeTree: A public knowledge-base of divergence times among organisms
-
DOI 10.1093/bioinformatics/btl505
-
Hedges SB, Dudley J, Kumar S (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22: 2971-2972. (Pubitemid 44811578)
-
(2006)
Bioinformatics
, vol.22
, Issue.23
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
70
-
-
0017272554
-
Enzyme recruitment in evolution of new function
-
Jensen RA (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
-
(1976)
Annu Rev Microbiol
, vol.30
, pp. 409-425
-
-
Jensen, R.A.1
-
71
-
-
84870687980
-
Evolution of minimal specificity and promiscuity in steroid hormone receptors
-
Eick GN, Colucci JK, Harms MJ, Ortlund EA, Thornton JW (2012) Evolution of minimal specificity and promiscuity in steroid hormone receptors. PLoS Genet 8: e1003072.
-
(2012)
PLoS Genet
, vol.8
-
-
Eick, G.N.1
Colucci, J.K.2
Harms, M.J.3
Ortlund, E.A.4
Thornton, J.W.5
-
72
-
-
0141431993
-
Resurrecting the ancestral steroid receptor: Ancient origin of estrogen signaling
-
DOI 10.1126/science.1086185
-
Thornton JW, Need E, Crews D (2003) Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301: 1714-1717. (Pubitemid 37174363)
-
(2003)
Science
, vol.301
, Issue.5640
, pp. 1714-1717
-
-
Thornton, J.W.1
Need, E.2
Crews, D.3
-
73
-
-
84879943516
-
Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors
-
Harms MJ, Eick GN, Goswami D, Colucci JK, Griffin PR, et al. (2013) Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors. Proc Natl Acad Sci U S A 110: 11475-11480.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 11475-11480
-
-
Harms, M.J.1
Eick, G.N.2
Goswami, D.3
Colucci, J.K.4
Griffin, P.R.5
-
74
-
-
1942531303
-
Resurrecting ancient genes: Experimental analysis of extinct molecules
-
Thornton JW (2004) Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet 5: 366-375.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 366-375
-
-
Thornton, J.W.1
-
75
-
-
23144448512
-
ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures
-
DOI 10.1093/nar/gki370
-
Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-302. (Pubitemid 44529930)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Landau, M.1
Mayrose, I.2
Rosenberg, Y.3
Glaser, F.4
Martz, E.5
Pupko, T.6
Ben-Tal, N.7
-
76
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38: W529-533.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
77
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
DOI 10.1006/jmbi.1996.0167
-
Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257: 342-358. (Pubitemid 26114038)
-
(1996)
Journal of Molecular Biology
, vol.257
, Issue.2
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
78
-
-
33747840720
-
ET viewer: An application for predicting and visualizing functional sites in protein structures
-
DOI 10.1093/bioinformatics/btl285
-
Morgan DH, Kristensen DM, Mittelman D, Lichtarge O (2006) ET viewer: an application for predicting and visualizing functional sites in protein structures. Bioinformatics 22: 2049-2050. (Pubitemid 44283020)
-
(2006)
Bioinformatics
, vol.22
, Issue.16
, pp. 2049-2050
-
-
Morgan, D.H.1
Kristensen, D.M.2
Mittelman, D.3
Lichtarge, O.4
-
80
-
-
77952356281
-
Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors
-
Rodriguez GJ, Yao R, Lichtarge O, Wensel TG (2010) Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc Natl Acad Sci U S A 107: 7787-7792.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 7787-7792
-
-
Rodriguez, G.J.1
Yao, R.2
Lichtarge, O.3
Wensel, T.G.4
-
81
-
-
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
-
82
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
DOI 10.1093/nar/gki025
-
Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33: D501-504. (Pubitemid 40207924)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
83
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
84
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
DOI 10.1093/bioinformatics/bti191
-
Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463. (Pubitemid 40310232)
-
(2005)
Bioinformatics
, vol.21
, Issue.4
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
85
-
-
42449090264
-
PROMALS3D: A tool for multiple protein sequence and structure alignments
-
DOI 10.1093/nar/gkn072
-
Pei J, Kim B-H, Grishin NV (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Research 36: 2295-2300. (Pubitemid 351567002)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.7
, pp. 2295-2300
-
-
Pei, J.1
Kim, B.-H.2
Grishin, N.V.3
-
86
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9: 40.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
87
-
-
34147143867
-
Structural Mechanism for the Fine-tuning of CcpA Function by The Small Molecule Effectors Glucose 6-Phosphate and Fructose 1,6-Bisphosphate
-
DOI 10.1016/j.jmb.2007.02.054, PII S0022283607002355
-
Schumacher MA, Seidel G, Hillen W, Brennan RG (2007) Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate. J Mol Biol 368: 1042-1050. (Pubitemid 46574658)
-
(2007)
Journal of Molecular Biology
, vol.368
, Issue.4
, pp. 1042-1050
-
-
Schumacher, M.A.1
Seidel, G.2
Hillen, W.3
Brennan, R.G.4
-
88
-
-
25144499763
-
Resmap: Automated representation of macromolecular interfaces as two-dimensional networks
-
DOI 10.1093/bioinformatics/bti511
-
Swint-Kruse L, Brown CS (2005) Resmap: automated representation of macromolecular interfaces as two-dimensional networks. Bioinformatics 21: 3327-3328. (Pubitemid 41418454)
-
(2005)
Bioinformatics
, vol.21
, Issue.15
, pp. 3327-3328
-
-
Swint-Kruse, L.1
Brown, C.S.2
-
89
-
-
13044272912
-
Automated analysis of interatomic contacts in proteins
-
DOI 10.1093/bioinformatics/15.4.327
-
Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics 15: 327-332. (Pubitemid 29213759)
-
(1999)
Bioinformatics
, vol.15
, Issue.4
, pp. 327-332
-
-
Sobolev, V.1
Sorokine, A.2
Prilusky, J.3
Abola, E.E.4
Edelman, M.5
-
90
-
-
0031564639
-
Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli
-
DOI 10.1006/jmbi.1996.0913
-
Izu H, Adachi O, Yamada M (1997) Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli. J Mol Biol 267: 778-793. (Pubitemid 27192653)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.4
, pp. 778-793
-
-
Izu, H.1
Adachi, O.2
Yamada, M.3
-
91
-
-
0031897881
-
Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by gntR and the cyclic AMP (cAMP)-cAMP receptor protein complex
-
Peekhaus N, Conway T (1998) Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex. J Bacteriol 180: 1777-1785. (Pubitemid 28173057)
-
(1998)
Journal of Bacteriology
, vol.180
, Issue.7
, pp. 1777-1785
-
-
Peekhaus, N.1
Conway, T.2
-
92
-
-
0031009431
-
Characterization of TreR, the major regulator of the Escherichia coli trehalose system
-
DOI 10.1074/jbc.272.20.13026
-
Horlacher R, Boos W (1997) Characterization of TreR, the major regulator of the Escherichia coli trehalose system. J Biol Chem 272: 13026-13032. (Pubitemid 27216722)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.20
, pp. 13026-13032
-
-
Horlacher, R.1
Boos, W.2
-
93
-
-
0032483005
-
NADP, corepressor for the Bacillus catabolite control protein CcpA
-
DOI 10.1073/pnas.95.16.9590
-
Kim JH, Voskuil MI, Chambliss GH (1998) NADP, corepressor for the Bacillus catabolite control protein CcpA. Proc Natl Acad Sci U S A 95: 9590-9595. (Pubitemid 28506276)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.16
, pp. 9590-9595
-
-
Kim, J.-H.1
Voskuil, M.I.2
Chambliss, G.H.3
-
94
-
-
0033582597
-
Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon
-
DOI 10.1006/jmbi.1998.2492
-
Galinier A, Deutscher J, Martin-Verstraete I (1999) Phosphorylation of either crh or HPr mediates binding of CcpA to the bacillus subtilis xyn cre and catabolite repression of the xyn operon. J Mol Biol 286: 307-314. (Pubitemid 29090151)
-
(1999)
Journal of Molecular Biology
, vol.286
, Issue.2
, pp. 307-314
-
-
Galinier, A.1
Deutscher, J.2
Martin-Verstraete, I.3
-
95
-
-
0028917215
-
Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in gram-positive bacteria
-
Deutscher J, Kuster E, Bergstedt U, Charrier V, Hillen W (1995) Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in gram-positive bacteria. Mol Microbiol 15: 1049-1053.
-
(1995)
Mol Microbiol
, vol.15
, pp. 1049-1053
-
-
Deutscher, J.1
Kuster, E.2
Bergstedt, U.3
Charrier, V.4
Hillen, W.5
-
96
-
-
0028364161
-
Loss of protein kinase-catalyzed phosphorylation of HPr, a phosphocarrier protein of the phosphotransferase system, by mutation of the ptsH gene confers catabolite repression resistance to several catabolic genes of Bacillus subtilis
-
Deutscher J, Reizer J, Fischer C, Galinier A, Saier MH Jr, et al. (1994) Loss of protein kinase-catalyzed phosphorylation of HPr, a phosphocarrier protein of the phosphotransferase system, by mutation of the ptsH gene confers catabolite repression resistance to several catabolic genes of Bacillus subtilis. J Bacteriol 176: 3336-3344. (Pubitemid 24166726)
-
(1994)
Journal of Bacteriology
, vol.176
, Issue.11
, pp. 3336-3344
-
-
Deutscher, J.1
Reizer, J.2
Fischer, C.3
Galinier, A.4
Saier Jr., M.H.5
Steinmetz, M.6
-
97
-
-
0023654073
-
Purification and properties of Gal repressor:PL-galR fusion in pKC31 plasmid vector
-
Majumdar A, Rudikoff S, Adhya S (1987) Purification and properties of Gal repressor:pL-galR fusion in pKC31 plasmid vector. J Biol Chem 262: 2326-2331.
-
(1987)
J Biol Chem
, vol.262
, pp. 2326-2331
-
-
Majumdar, A.1
Rudikoff, S.2
Adhya, S.3
-
98
-
-
0025182048
-
Purification of the Escherichia coli purine regulon repressor and identification of corepressors
-
Rolfes RJ, Zalkin H (1990) Purification of the Escherichia coli purine regulon repressor and identification of corepressors. J Bacteriol 172: 5637-5642. (Pubitemid 20317096)
-
(1990)
Journal of Bacteriology
, vol.172
, Issue.10
, pp. 5637-5642
-
-
Rolfes, R.J.1
Zalkin, H.2
-
99
-
-
0024263352
-
Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator
-
Rolfes RJ, Zalkin H (1988) Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator. J Biol Chem 263: 19653-19661. (Pubitemid 19016448)
-
(1988)
Journal of Biological Chemistry
, vol.263
, Issue.36
, pp. 19653-19661
-
-
Rolfes, R.J.1
Zalkin, H.2
-
100
-
-
0022353006
-
Regulation of Escherichia coli purF. Analysis of the control region of a pur regulon gene
-
Makaroff CA, Zalkin H (1985) Regulation of Escherichia coli purF. Analysis of the control region of a pur regulon gene. J Biol Chem 260: 10378-10387.
-
(1985)
J Biol Chem
, vol.260
, pp. 10378-10387
-
-
Makaroff, C.A.1
Zalkin, H.2
-
101
-
-
0027087375
-
Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli
-
Mauzy CA, Hermodson MA (1992) Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli. Protein Sci 1: 831-842. (Pubitemid 23007321)
-
(1992)
Protein Science
, vol.1
, Issue.7
, pp. 831-842
-
-
Mauzy, C.A.1
Hermodson, M.A.2
-
102
-
-
0021364453
-
D-ribose metabolism in Escherichia coli K-12: Genetics, regulation, and transport
-
Lopilato JE, Garwin JL, Emr SD, Silhavy TJ, Beckwith JR (1984) D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. J Bacteriol 158: 665-673. (Pubitemid 14145669)
-
(1984)
Journal of Bacteriology
, vol.158
, Issue.2
, pp. 665-673
-
-
Lopilato, J.E.1
Garwin, J.L.2
Emr, S.D.3
-
103
-
-
0027050193
-
Structural homology between rbs repressor and ribose binding protein implies functional similarity
-
Mauzy CA, Hermodson MA (1992) Structural homology between rbs repressor and ribose binding protein implies functional similarity. Protein Sci 1: 843-849. (Pubitemid 23007322)
-
(1992)
Protein Science
, vol.1
, Issue.7
, pp. 843-849
-
-
Mauzy, C.A.1
Hermodson, M.A.2
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