-
2
-
-
1842861592
-
Structure, function and evolution of multidomain proteins
-
Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA (2004) Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 14:208-216.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 208-216
-
-
Vogel, C.1
Bashton, M.2
Kerrison, N.D.3
Chothia, C.4
Teichmann, S.A.5
-
3
-
-
0032509105
-
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
-
Park J, et al. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 284:1201-1210.
-
(1998)
J Mol Biol
, vol.284
, pp. 1201-1210
-
-
Park, J.1
-
4
-
-
29244447181
-
Kalign-an accurate and fast multiple sequence alignment algorithm
-
Lassmann T, Sonnhammer EL (2005) Kalign-an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6:298.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 298
-
-
Lassmann, T.1
Sonnhammer, E.L.2
-
5
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
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.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
6
-
-
25644442464
-
Natural-like function in artificial WW domains
-
Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R (2005) Natural-like function in artificial WW domains. Nature 437:579-583.
-
(2005)
Nature
, vol.437
, pp. 579-583
-
-
Russ, W.P.1
Lowery, D.M.2
Mishra, P.3
Yaffe, M.B.4
Ranganathan, R.5
-
7
-
-
25644452032
-
Evolutionary information for specifying a protein fold
-
Socolich M, et al. (2005) Evolutionary information for specifying a protein fold. Nature 437:512-518.
-
(2005)
Nature
, vol.437
, pp. 512-518
-
-
Socolich, M.1
-
8
-
-
34547499110
-
The design and characterization of two proteins with 88% sequence identity but different structure and function
-
Alexander PA, He Y, Chen Y, Orban J, Bryan PN (2007) The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci USA 104:11963-11968.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 11963-11968
-
-
Alexander, P.A.1
He, Y.2
Chen, Y.3
Orban, J.4
Bryan, P.N.5
-
9
-
-
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
-
10
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
11
-
-
0035937260
-
Pairwise sequence alignment below the twilight zone
-
Blake JD, Cohen FE (2001) Pairwise sequence alignment below the twilight zone. J Mol Biol 307:721-735.
-
(2001)
J Mol Biol
, vol.307
, pp. 721-735
-
-
Blake, J.D.1
Cohen, F.E.2
-
12
-
-
0022550940
-
Identification of protein sequence homology by consensus template alignment
-
Taylor WR (1986) Identification of protein sequence homology by consensus template alignment. J Mol Biol 188:233-258.
-
(1986)
J Mol Biol
, vol.188
, pp. 233-258
-
-
Taylor, W.R.1
-
13
-
-
0027994453
-
Recognition of related proteins by iterative template refinement (ITR)
-
Yi TM, Lander ES (1994) Recognition of related proteins by iterative template refinement (ITR). Protein Sci 3:1315-1328.
-
(1994)
Protein Sci
, vol.3
, pp. 1315-1328
-
-
Yi, T.M.1
Lander, E.S.2
-
15
-
-
0028158905
-
Improving the sensitivity of the sequence profile method
-
Luthy R, Xenarios I, Bucher P (1994) Improving the sensitivity of the sequence profile method. Protein Sci 3:139-146.
-
(1994)
Protein Sci
, vol.3
, pp. 139-146
-
-
Luthy, R.1
Xenarios, I.2
Bucher, P.3
-
16
-
-
0030322814
-
A study of combined structure/sequence profiles
-
Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D (1996) A study of combined structure/sequence profiles. Fold Des 1:451-461.
-
(1996)
Fold Des
, vol.1
, pp. 451-461
-
-
Elofsson, A.1
Fischer, D.2
Rice, D.W.3
Le Grand, S.M.4
Eisenberg, D.5
-
18
-
-
0030925920
-
Pfam: A comprehensive database of protein domain families based on seed alignments
-
Sonnhammer EL, Eddy SR, Durbin R (1997) Pfam: A comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420.
-
(1997)
Proteins
, vol.28
, pp. 405-420
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Durbin, R.3
-
19
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
20
-
-
33646170322
-
Weak pairwise correlations imply strongly correlated network states in a neural population
-
Schneidman E, Berry MJ, Segev R, Bialek W (2006) Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 440:1007-1012.
-
(2006)
Nature
, vol.440
, pp. 1007-1012
-
-
Schneidman, E.1
Berry, M.J.2
Segev, R.3
Bialek, W.4
-
22
-
-
51649119022
-
-
Phylogenetic profiles as a unified framework for measuring protein structure, function and evolution, arXiv:0806.239, q-bio.Q
-
Ko KD, et al. (2008) Phylogenetic profiles as a unified framework for measuring protein structure, function and evolution. Phys Arch arXiv:0806.239, q-bio.Q.
-
(2008)
Phys Arch
-
-
Ko, K.D.1
-
23
-
-
43049094016
-
The diversity of retrotransposons and the properties of their reverse transcriptases
-
Eickbush TH, Jamburuthugoda VK (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134:221-234.
-
(2008)
Virus Res
, vol.134
, pp. 221-234
-
-
Eickbush, T.H.1
Jamburuthugoda, V.K.2
-
24
-
-
0141742359
-
The unusual phylogenetic distribution of retrotransposons: A hypothesis
-
Boeke JD (2003) The unusual phylogenetic distribution of retrotransposons: A hypothesis. Genome Res 13:1975-1983.
-
(2003)
Genome Res
, vol.13
, pp. 1975-1983
-
-
Boeke, J.D.1
-
25
-
-
0014964654
-
RNA-dependent DNA polymerase in virions of RNA tumour viruses
-
Baltimore D (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature 226:1209-1211.
-
(1970)
Nature
, vol.226
, pp. 1209-1211
-
-
Baltimore, D.1
-
27
-
-
0025006614
-
Origin and evolution of retroelements based upon their reverse transcriptase sequences
-
Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353-3362.
-
(1990)
EMBO J
, vol.9
, pp. 3353-3362
-
-
Xiong, Y.1
Eickbush, T.H.2
-
29
-
-
0024784519
-
Identification of four conserved motifs among the RNA-dependent polymerase encoding elements
-
Poch O, Sauvaget I, Delarue M, Tordo N (1989) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J 8:3867-3874.
-
(1989)
EMBO J
, vol.8
, pp. 3867-3874
-
-
Poch, O.1
Sauvaget, I.2
Delarue, M.3
Tordo, N.4
-
30
-
-
0026693137
-
Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
-
Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA (1992) Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783-1790.
-
(1992)
Science
, vol.256
, pp. 1783-1790
-
-
Kohlstaedt, L.A.1
Wang, J.2
Friedman, J.M.3
Rice, P.A.4
Steitz, T.A.5
-
31
-
-
0034917751
-
Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses
-
Malik HS, Eickbush TH (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11:1187-1197.
-
(2001)
Genome Res
, vol.11
, pp. 1187-1197
-
-
Malik, H.S.1
Eickbush, T.H.2
-
32
-
-
0034100186
-
Multiple LTR-retrotransposon families in the asexual yeast Candida albicans
-
Goodwin TJ, Poulter RT (2000) Multiple LTR-retrotransposon families in the asexual yeast Candida albicans. Genome Res 10:174-191.
-
(2000)
Genome Res
, vol.10
, pp. 174-191
-
-
Goodwin, T.J.1
Poulter, R.T.2
-
33
-
-
4644280174
-
Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements
-
Doulatov S, et al. (2004) Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 431:476-481.
-
(2004)
Nature
, vol.431
, pp. 476-481
-
-
Doulatov, S.1
-
35
-
-
33644845048
-
Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
-
Kim Y, Subramaniam S (2006) Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins 62:1115-1124.
-
(2006)
Proteins
, vol.62
, pp. 1115-1124
-
-
Kim, Y.1
Subramaniam, S.2
-
36
-
-
36949020644
-
Predicting protein function with hierarchical phylogenetic profiles: The Gene3D Phylo-Tuner method applied to eukaryotic genomes
-
Ranea JA, Yeats C, Grant A, Orengo CA (2007) Predicting protein function with hierarchical phylogenetic profiles: The Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoS Comput Biol 3:e237.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Ranea, J.A.1
Yeats, C.2
Grant, A.3
Orengo, C.A.4
-
37
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci USA 96:4285-4288.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
38
-
-
0345864022
-
SMART 4.0: Towards genomic data integration
-
Letunic I, et al. (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res 32:D142-D144.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Letunic, I.1
-
39
-
-
13444262384
-
CDD: A conserved domain database for protein classification
-
Marchler-Bauer A, et al. (2005) CDD: A conserved domain database for protein classification. Nucleic Acids Res 33:D192-D196.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Marchler-Bauer, A.1
-
40
-
-
14544307864
-
Phospholipase Cgamma1 controls surface expression of TRPC3 through an intermolecular PH domain
-
van Rossum DB, et al. (2005) Phospholipase Cgamma1 controls surface expression of TRPC3 through an intermolecular PH domain. Nature 434:99-104.
-
(2005)
Nature
, vol.434
, pp. 99-104
-
-
van Rossum, D.B.1
-
41
-
-
33749646106
-
Action of TFII-I outside the nucleus as an inhibitor of agonist-induced calcium entry
-
Caraveo G, van Rossum DB, Patterson RL, Snyder SH, Desiderio S (2006) Action of TFII-I outside the nucleus as an inhibitor of agonist-induced calcium entry. Science 314:122-125.
-
(2006)
Science
, vol.314
, pp. 122-125
-
-
Caraveo, G.1
van Rossum, D.B.2
Patterson, R.L.3
Snyder, S.H.4
Desiderio, S.5
-
42
-
-
51649118280
-
Ancient origin of the new developmental superfamily DANGER
-
Nikolaidis N, et al. (2007) Ancient origin of the new developmental superfamily DANGER. PLoS ONE 2:e204.
-
(2007)
PLoS ONE
, vol.2
-
-
Nikolaidis, N.1
-
43
-
-
39549102614
-
HSP90 regulates cell survival via inositol hexakisphosphate kinase-2
-
Chakraborty A, et al. (2008) HSP90 regulates cell survival via inositol hexakisphosphate kinase-2. Proc Natl Acad Sci USA 105:1134-1139.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 1134-1139
-
-
Chakraborty, A.1
-
44
-
-
34547781750
-
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
-
-
-
-
45
-
-
0030819894
-
Telomerase catalytic subunit homologs from fission yeast and human
-
Nakamura TM, et al. (1997) Telomerase catalytic subunit homologs from fission yeast and human. Science 277:955-959.
-
(1997)
Science
, vol.277
, pp. 955-959
-
-
Nakamura, T.M.1
-
46
-
-
0031574072
-
The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
47
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar RC (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
48
-
-
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
-
49
-
-
33747818327
-
Kalign, Kalignvu and Mumsa: Web servers for multiple sequence alignment
-
Lassmann T, Sonnhammer EL (2006) Kalign, Kalignvu and Mumsa: Web servers for multiple sequence alignment. Nucleic Acids Res 34:W596-W599.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Lassmann, T.1
Sonnhammer, E.L.2
-
50
-
-
3242891684
-
DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ
-
Morgenstern B (2004) DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res 32(Web Server issue):W33-6.
-
(2004)
Nucleic Acids Res 32(Web Server issue)
-
-
Morgenstern, B.1
-
51
-
-
0033179990
-
Linear mitochondrial plasmids of F. oxysporum are novel, telomere-like retroelements
-
Walther TC, Kennell JC (1999) Linear mitochondrial plasmids of F. oxysporum are novel, telomere-like retroelements. Mol Cell 4:229-238.
-
(1999)
Mol Cell
, vol.4
, pp. 229-238
-
-
Walther, T.C.1
Kennell, J.C.2
-
52
-
-
0034532823
-
Tca5, a Ty5-like retrotransposon from Candida albicans
-
Plant EP, Goodwin TJ, Poulter RT (2000) Tca5, a Ty5-like retrotransposon from Candida albicans. Yeast 16:1509-1518.
-
(2000)
Yeast
, vol.16
, pp. 1509-1518
-
-
Plant, E.P.1
Goodwin, T.J.2
Poulter, R.T.3
|