-
1
-
-
0033977832
-
Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis
-
and
-
Atchley W.R., Wollenberg K.R., Fitch W.M., Terhalle W., and Dress A.W., 2000. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol., 17: 164–78.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 164-178
-
-
Atchley, W.R.1
Wollenberg, K.R.2
Fitch, W.M.3
Terhalle, W.4
Dress, A.W.5
-
2
-
-
0030707656
-
Structural plasticity in a remodeled protein-protein interface
-
and
-
Atwell S., Ultsch M., de Vos A.M., and Wells J.A., 1997. Structural plasticity in a remodeled protein-protein interface. Science, 278: 1125–8.
-
(1997)
Science
, vol.278
, pp. 1125-1128
-
-
Atwell, S.1
Ultsch, M.2
de Vos, A.M.3
Wells, J.A.4
-
3
-
-
0346750651
-
Statistical properties of neutral evolution
-
and, (Sul
-
Bastolla U., Porto M., Roman H.E., and Vendruscolo M., 2003. Statistical properties of neutral evolution. J. Mol. Evol., 57(Suppl 1): S103–119.
-
(2003)
J. Mol. Evol
, vol.57
, Issue.1
, pp. S103-S119
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
4
-
-
0034635955
-
A statistical mechanical method to optimize energy functions for protein folding
-
and
-
Bastolla U., Vendruscolo M., and Knapp E.W., 2000. A statistical mechanical method to optimize energy functions for protein folding. Proc. Natl. Acad. Sci. U.S.A., 97: 3977–81.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 3977-3981
-
-
Bastolla, U.1
Vendruscolo, M.2
Knapp, E.W.3
-
6
-
-
20444426807
-
Networks of coevolving sites in structural and functional domains of serpin proteins
-
and
-
Buck M.J., and Atchley W.R., 2005. Networks of coevolving sites in structural and functional domains of serpin proteins. Mol. Biol. Evol., 22: 1627–34.
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 1627-1634
-
-
Buck, M.J.1
Atchley, W.R.2
-
7
-
-
0030970646
-
An analysis of simultaneous variation in protein structures
-
and
-
Chelvanayagam G., Eggenschwilker A., Knecht L., Gonnet G.H., and Benner S.A., 1997. An analysis of simultaneous variation in protein structures. Protein Engineering, 10: 307–16.
-
(1997)
Protein Engineering
, vol.10
, pp. 307-316
-
-
Chelvanayagam, G.1
Eggenschwilker, A.2
Knecht, L.3
Gonnet, G.H.4
Benner, S.A.5
-
8
-
-
33748701649
-
Detecting functional modules in the yeast protein-protein interaction network
-
and
-
Chen J., and Yuan B., 2006. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics, 22: 2283–90.
-
(2006)
Bioinformatics
, vol.22
, pp. 2283-2290
-
-
Chen, J.1
Yuan, B.2
-
9
-
-
33745622668
-
An effective structure learning method for constructing gene networks
-
and
-
Chen X-W., Anantha G., and Wang X., 2006. An effective structure learning method for constructing gene networks. Bioinformatics, 22: 1367–74.
-
(2006)
Bioinformatics
, vol.22
, pp. 1367-1374
-
-
Chen, X.-W.1
Anantha, G.2
Wang, X.3
-
10
-
-
28444463255
-
Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
-
and
-
Choi S.S., Li W., and Lahn B.T., 2005. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nat. Genet., 37: 1367–71.
-
(2005)
Nat. Genet
, vol.37
, pp. 1367-1371
-
-
Choi, S.S.1
Li, W.2
Lahn, B.T.3
-
11
-
-
0028832687
-
Covariation residues in the homeodomain sequence family
-
Clarke N.D., 1995. Covariation residues in the homeodomain sequence family. Protein Sci., 4: 2269–78.
-
(1995)
Protein Sci
, vol.4
, pp. 2269-2278
-
-
Clarke, N.D.1
-
12
-
-
33744940805
-
Adaptative Covariation between the coat and the movement proteins of Prunus Necrotic Ringspot Virus
-
and
-
Codoñer F.M., Fares M.A., and Elena S.F., 2006. Adaptative Covariation between the coat and the movement proteins of Prunus Necrotic Ringspot Virus. J. Virol., 80: 5833–40.
-
(2006)
J. Virol
, vol.80
, pp. 5833-5840
-
-
Codoñer, F.M.1
Fares, M.A.2
Elena, S.F.3
-
13
-
-
0032169271
-
Conservation of gene order: a fingerprint of proteins that physically interact
-
and
-
Dandekar T., Snel B., Huynen M., and Bork P., 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23: 324–8.
-
(1998)
Trends Biochem. Sci
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
14
-
-
0041358614
-
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
-
and
-
Date S.V., and Marcotte E.M., 2003. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnol., 21: 1055–62.
-
(2003)
Nature Biotechnol
, vol.21
, pp. 1055-1062
-
-
Date, S.V.1
Marcotte, E.M.2
-
15
-
-
0036799752
-
Inferring Domain-Domain interactions from protein-protein interactions
-
and
-
Deng M., Mehta S., Sun F., and Chen T., 2002. Inferring Domain-Domain interactions from protein-protein interactions. Genome Research, 12: 1540–8.
-
(2002)
Genome Research
, vol.12
, pp. 1540-1548
-
-
Deng, M.1
Mehta, S.2
Sun, F.3
Chen, T.4
-
16
-
-
84860533518
-
Detecting coevolving amino acid sites using Bayesian mutational mapping
-
and
-
Dimmic M.W., Hubisz M.J., Bustamante C.D., and Nielsen R., 2005. Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics, 21: i126–35.
-
(2005)
Bioinformatics
, vol.21
, pp. i126-i135
-
-
Dimmic, M.W.1
Hubisz, M.J.2
Bustamante, C.D.3
Nielsen, R.4
-
17
-
-
0026736363
-
Determination of eukaryotic protein coding regions using neutral networks and information theory
-
and
-
Farber R., Lapedes A., and Sirotkin K., 1992. Determination of eukaryotic protein coding regions using neutral networks and information theory. J. Mol. Biol., 226: 471–9.
-
(1992)
J. Mol. Biol
, vol.226
, pp. 471-479
-
-
Farber, R.1
Lapedes, A.2
Sirotkin, K.3
-
18
-
-
33750998062
-
Computational and statistical methods to explore the various dimensions of protein evolution
-
Fares M.A., 2006. Computational and statistical methods to explore the various dimensions of protein evolution. Curr. Bioinf., 1: 207–17.
-
(2006)
Curr. Bioinf
, vol.1
, pp. 207-217
-
-
Fares, M.A.1
-
19
-
-
33751017993
-
CAPS: Coevolution Analysis using Protein Sequences
-
and
-
Fares M.A., and McNally D., 2006. CAPS: Coevolution Analysis using Protein Sequences. Bioinformatics, 22: 2821–2.
-
(2006)
Bioinformatics
, vol.22
, pp. 2821-2822
-
-
Fares, M.A.1
McNally, D.2
-
20
-
-
33744457709
-
A novel method for detecting intra-molecular coevolution: adding a further dimension to selective constraints analyses
-
and
-
Fares M.A., and Travers S.A.A., 2006. A novel method for detecting intra-molecular coevolution: adding a further dimension to selective constraints analyses. Genetics, 173: 9–23.
-
(2006)
Genetics
, vol.173
, pp. 9-23
-
-
Fares, M.A.1
Travers, S.A.A.2
-
21
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein J., 1985. Phylogenies and the comparative method. Am. Nat., 15: 1–15.
-
(1985)
Am. Nat
, vol.15
, pp. 1-15
-
-
Felsenstein, J.1
-
22
-
-
0015162378
-
Rate of change of concomitantly variable codons
-
Fitch W.M., 1971. Rate of change of concomitantly variable codons. J. Mol. Evol., 1: 84–96.
-
(1971)
J. Mol. Evol
, vol.1
, pp. 84-96
-
-
Fitch, W.M.1
-
23
-
-
0014860857
-
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem
-
and
-
Fitch W.M., and Markowitz E., 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution Biochem. Genetics, 4: 579–3.
-
(1970)
Genetics
, vol.4
, pp. 579-573
-
-
Fitch, W.M.1
Markowitz, E.2
-
24
-
-
3042842115
-
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
-
and
-
Fodor A. A., and Aldrich R. W., 2004. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins, 56: 211–21.
-
(2004)
Proteins
, vol.56
, pp. 211-221
-
-
Fodor, A.A.1
Aldrich, R.W.2
-
25
-
-
2942695714
-
Coevolution of gene expression among interacting proteins
-
and
-
Fraser H.B., Hirsh A.E., Wall D.P., and Eisen M.B., 2004. Coevolution of gene expression among interacting proteins. Proc. Natl. Acad. Sci. U.S.A., 101: 9033–8.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.101
, pp. 9033-9038
-
-
Fraser, H.B.1
Hirsh, A.E.2
Wall, D.P.3
Eisen, M.B.4
-
26
-
-
0036145469
-
Persistently conserved positions in structurally similar, sequences dissimilar proteins: roles in preserving protein fold and function
-
and
-
Friedber I., and Margalit H., 2002. Persistently conserved positions in structurally similar, sequences dissimilar proteins: roles in preserving protein fold and function. Protein Sci., 11: 350–60.
-
(2002)
Protein Sci
, vol.11
, pp. 350-360
-
-
Friedber, I.1
Margalit, H.2
-
27
-
-
0030249746
-
The coevolution of gene family trees
-
Fryxell K.J., 1996. The coevolution of gene family trees. Trends Genet., 12: 364–9.
-
(1996)
Trends Genet
, vol.12
, pp. 364-369
-
-
Fryxell, K.J.1
-
28
-
-
0036301488
-
Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences
-
and
-
Fukami-Kobayashi K., Schreiber D.R., and Benner S.A., 2002. Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J. Mol. Biol., 319: 729–43.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 729-743
-
-
Fukami-Kobayashi, K.1
Schreiber, D.R.2
Benner, S.A.3
-
29
-
-
18544362952
-
Mutual information in protein multiple alignments reveals two classes of coevolving positions
-
and
-
Gloor G.B., Martin L.C., Wahl L.M., and Dunn S.D., 2005. Mutual information in protein multiple alignments reveals two classes of coevolving positions. Biochemistry, 44: 7156–65.
-
(2005)
Biochemistry
, vol.44
, pp. 7156-7165
-
-
Gloor, G.B.1
Martin, L.C.2
Wahl, L.M.3
Dunn, S.D.4
-
30
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
and
-
Göbel U., Sander C., Schneider R., and Valencia A., 1994. Correlated mutations and residue contacts in proteins. Proteins, 18: 309–17.
-
(1994)
Proteins
, vol.18
, pp. 309-317
-
-
Göbel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
31
-
-
0034595516
-
Coevolution of proteins with their interaction partners
-
and
-
Goh Ch S., Bogan A.A., Joachimiak M., Walther D., and Cohen F.E., 2000. Coevolution of proteins with their interaction partners. J. Mol. Biol., 299: 283–93.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 283-293
-
-
Goh Ch, S.1
Bogan, A.A.2
Joachimiak, M.3
Walther, D.4
Cohen, F.E.5
-
32
-
-
0036435908
-
Coevolutionary analysis reveals insights into protein-protein interactions
-
and
-
Goh Ch S., and Cohen F.E., 2002. Coevolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol., 324: 177–92.
-
(2002)
J. Mol. Biol
, vol.324
, pp. 177-192
-
-
Goh Ch, S.1
Cohen, F.E.2
-
33
-
-
4043170491
-
Protein contact prediction using paterns of correlation
-
and
-
Hamilton N., Burrage K., Ragan M.A., and Huber T., 2004. Protein contact prediction using paterns of correlation. Proteins, 56: 679–84.
-
(2004)
Proteins
, vol.56
, pp. 679-684
-
-
Hamilton, N.1
Burrage, K.2
Ragan, M.A.3
Huber, T.4
-
34
-
-
0141571239
-
Covariation of amino acid positions in HIV-protease
-
and
-
Hoffman N.G., Schiffer C.A., and Swanstrom R., 2003. Covariation of amino acid positions in HIV-protease. Virology, 314: 536–48.
-
(2003)
Virology
, vol.314
, pp. 536-548
-
-
Hoffman, N.G.1
Schiffer, C.A.2
Swanstrom, R.3
-
35
-
-
0023764283
-
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
-
and
-
Hughes A. L., and Nei M., 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature, 335: 167–170.
-
(1988)
Nature
, vol.335
, pp. 167-170
-
-
Hughes, A.L.1
Nei, M.2
-
36
-
-
25444465885
-
Species-specific analysis of protein sequence motifs using mutual information
-
and
-
Hummel J., Keshvari N., Weckwerth W., and Selbig J., 2005. Species-specific analysis of protein sequence motifs using mutual information. BMC Bioinformatics, 6: 164–70.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 164-170
-
-
Hummel, J.1
Keshvari, N.2
Weckwerth, W.3
Selbig, J.4
-
37
-
-
0000371962
-
When is it coevolution?
-
Janzen D.H., 1980. When is it coevolution?. Evolution, 34: 611–2.
-
(1980)
Evolution
, vol.34
, pp. 611-612
-
-
Janzen, D.H.1
-
38
-
-
33748333117
-
Coevolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions
-
and
-
Jothi R., Cherukuri P.F., Tansneem A., and Przytycka T.M., 2006. Coevolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J. Mol. Biol., 362: 861–75.
-
(2006)
J. Mol. Biol
, vol.362
, pp. 861-875
-
-
Jothi, R.1
Cherukuri, P.F.2
Tansneem, A.3
Przytycka, T.M.4
-
39
-
-
0037311772
-
Visualization and analysis of protein interactions
-
and
-
Ju B.-H., Park B., Park J.H., and Han K., 2003. Visualization and analysis of protein interactions. Bioinformatics, 19: 317–8.
-
(2003)
Bioinformatics
, vol.19
, pp. 317-318
-
-
Ju, B.-H.1
Park, B.2
Park, J.H.3
Han, K.4
-
40
-
-
2442646432
-
Large-scale coevolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
-
and
-
Kim W.K., Bolser D.M., and Park J.H., 2004. Large-scale coevolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics, 20: 1138–50.
-
(2004)
Bioinformatics
, vol.20
, pp. 1138-1150
-
-
Kim, W.K.1
Bolser, D.M.2
Park, J.H.3
-
41
-
-
30344442462
-
Inferring functional information from domain coevolution
-
and
-
Kim Y., Koyutürk M., Topkara U., Grama A., and Subramaniam S., 2006. Inferring functional information from domain coevolution. Bioinformatics, 22: 40–9.
-
(2006)
Bioinformatics
, vol.22
, pp. 40-49
-
-
Kim, Y.1
Koyutürk, M.2
Topkara, U.3
Grama, A.4
Subramaniam, S.5
-
42
-
-
33644845048
-
Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
-
and
-
Kim Y., and Subramaniam S., 2006. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins, 62: 1115–24.
-
(2006)
Proteins
, vol.62
, pp. 1115-1124
-
-
Kim, Y.1
Subramaniam, S.2
-
43
-
-
0014421064
-
Evolutionary rate at the molecular level
-
Kimura M., 1968. Evolutionary rate at the molecular level. Nature, 217: 624–626.
-
(1968)
Nature
, vol.217
, pp. 624-626
-
-
Kimura, M.1
-
44
-
-
0027297096
-
Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis
-
and
-
Korber B.T., Farber R.M., Wolpert D.H., and Lapedes A.S., 1993. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. U.S.A., 90: 7176–80.
-
(1993)
Proc. Natl. Acad. Sci. U.S.A
, vol.90
, pp. 7176-7180
-
-
Korber, B.T.1
Farber, R.M.2
Wolpert, D.H.3
Lapedes, A.S.4
-
46
-
-
27944458910
-
Using information theory to search for co-evolving residues in proteins
-
and
-
Martin L.C., Gloor G.B., Dunn S.D., and Wahl L.M., 2005. Using information theory to search for co-evolving residues in proteins. Bioinformatics, 21: 4116–24.
-
(2005)
Bioinformatics
, vol.21
, pp. 4116-4124
-
-
Martin, L.C.1
Gloor, G.B.2
Dunn, S.D.3
Wahl, L.M.4
-
47
-
-
23344451687
-
Structure, function and evolution of transient and obligate protein-protein interactions
-
and
-
Mintseris J., and Weng Z., 2005. Structure, function and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci. U.S.A., 102: 10930–5.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
48
-
-
0345062357
-
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function
-
and
-
Mirny L.A., and Shakhnovich E.L., 1999. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol., 291: 177–96.
-
(1999)
J. Mol. Biol
, vol.291
, pp. 177-196
-
-
Mirny, L.A.1
Shakhnovich, E.L.2
-
49
-
-
0028330517
-
Coevolution of ligand-receptor pairs
-
and
-
Moyle W.R., Campbell R.K., Myers R.V., Bernard M.P., Han Y., and Wang X., 1994. Coevolution of ligand-receptor pairs. Nature, 368: 251–5.
-
(1994)
Nature
, vol.368
, pp. 251-255
-
-
Moyle, W.R.1
Campbell, R.K.2
Myers, R.V.3
Bernard, M.P.4
Han, Y.5
Wang, X.6
-
50
-
-
0028125904
-
How frequent are correlated changes in families of protein sequences?
-
Neher E., 1994. How frequent are correlated changes in families of protein sequences?. Proc. Natl. Acad. Sci. U.S.A., 91: 98–102.
-
(1994)
Proc. Natl. Acad. Sci. U.S.A
, vol.91
, pp. 98-102
-
-
Neher, E.1
-
51
-
-
29144462537
-
In silico identification of functional regions in proteins
-
and
-
Nimrod G., Glaser F., Steinberg D., Ben-Tal N., and Pupko T., 2005. In silico identification of functional regions in proteins. Bioinformatics, 21: i328–37.
-
(2005)
Bioinformatics
, vol.21
, pp. i328-i337
-
-
Nimrod, G.1
Glaser, F.2
Steinberg, D.3
Ben-Tal, N.4
Pupko, T.5
-
52
-
-
0037020282
-
Correlated mutation analyses on very large sequence families
-
and
-
Olivera L., Paiva A.C.M., and Vriend G., 2002. Correlated mutation analyses on very large sequence families. ChemBioChem., 3: 1010–7.
-
(2002)
ChemBioChem
, vol.3
, pp. 1010-1017
-
-
Olivera, L.1
Paiva, A.C.M.2
Vriend, G.3
-
53
-
-
0041418225
-
Identification of functionally conserved residues with the use of entropy-variability plots
-
and
-
Oliveira L., Paiva A.C.M., Paiva G., and Vriend G., 2003. Identification of functionally conserved residues with the use of entropy-variability plots. Proteins, 52: 544–52.
-
(2003)
Proteins
, vol.52
, pp. 544-552
-
-
Oliveira, L.1
Paiva, A.C.M.2
Paiva, G.3
Vriend, G.4
-
54
-
-
0028097770
-
Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters
-
Pagel M., 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. Roy. Soc. London ser. B., 255: 37–45.
-
(1994)
Proc. Roy. Soc. London ser. B
, vol.255
, pp. 37-45
-
-
Pagel, M.1
-
55
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
and
-
Pazos F., and Valencia A., 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering, 14: 609–14.
-
(2001)
Protein Engineering
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
56
-
-
0036568319
-
In silico two-hybrid system for Selection of physically interacting protein pairs
-
and
-
Pazos F., and Valencia A., 2002. In silico two-hybrid system for Selection of physically interacting protein pairs. Proteins, 47: 219–27.
-
(2002)
Proteins
, vol.47
, pp. 219-227
-
-
Pazos, F.1
Valencia, A.2
-
57
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
and
-
Pazos F., Helmer-Citterich M., Ausiello G., and Valencia A., 1997. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271: 511–23.
-
(1997)
J. Mol. Biol
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
Valencia, A.4
-
58
-
-
24644502565
-
Assessing protein coevolution in the context of the tree life assists in the prediction of the interactome
-
and
-
Pazos F., Ranea J.A.G., Juan D., and Strenberg M.J.E., 2005. Assessing protein coevolution in the context of the tree life assists in the prediction of the interactome. J. Mol. Biol., 352: 1002–15.
-
(2005)
J. Mol. Biol
, vol.352
, pp. 1002-1015
-
-
Pazos, F.1
Ranea, J.A.G.2
Juan, D.3
Strenberg, M.J.E.4
-
59
-
-
32144442848
-
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
-
and
-
Pei J., Cai W., Kinc L.N., and Grishin N.V., 2006. Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinformatics, 22: 164–71.
-
(2006)
Bioinformatics
, vol.22
, pp. 164-171
-
-
Pei, J.1
Cai, W.2
Kinc, L.N.3
Grishin, N.V.4
-
60
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
-
and
-
Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., and Yeates T.O., 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A., 96: 4285–8.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
61
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
and
-
Pollock D.D., and Taylor W.R., 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Engineering, 6: 647–57.
-
(1997)
Protein Engineering
, vol.6
, pp. 647-657
-
-
Pollock, D.D.1
Taylor, W.R.2
-
62
-
-
0033582946
-
Coevolving protein residues: maximum likelihood identification and relationship to structure
-
and
-
Pollock D.D., Taylor W.R., and Goldman N., 1999. Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol., 287: 187–98.
-
(1999)
J. Mol. Biol
, vol.287
, pp. 187-198
-
-
Pollock, D.D.1
Taylor, W.R.2
Goldman, N.3
-
63
-
-
0034794239
-
Evaluation of a anovel method for the identification of coevolving protein residues
-
and
-
Pritchard L., Bladon P., Mitchell J.M.O., and Dufton M.J., 2001. Evaluation of a anovel method for the identification of coevolving protein residues. Protein Engineering, 14: 549–55.
-
(2001)
Protein Engineering
, vol.14
, pp. 549-555
-
-
Pritchard, L.1
Bladon, P.2
Mitchell, J.M.O.3
Dufton, M.J.4
-
64
-
-
0037436412
-
Exploiting the coevolution of interacting proteins to discover interaction specificity
-
and
-
Ramani A.K., and Marcotte E.M., 2003. Exploiting the coevolution of interacting proteins to discover interaction specificity. J. Mol. Biol., 327: 273–84.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 273-284
-
-
Ramani, A.K.1
Marcotte, E.M.2
-
65
-
-
0029091043
-
Estimating substitution rates in ribosomal RNA genes
-
Rzhetsky A., 1995. Estimating substitution rates in ribosomal RNA genes. Mol. Biol. Evol., 141: 771–83.
-
(1995)
Mol. Biol. Evol
, vol.141
, pp. 771-783
-
-
Rzhetsky, A.1
-
66
-
-
0027288463
-
The HSSP data base of protein structure-sequence alignments
-
and
-
Sander C., and Schneider R., 1993. The HSSP data base of protein structure-sequence alignments. Nucleic Acid Res., 21: 3105–9.
-
(1993)
Nucleic Acid Res
, vol.21
, pp. 3105-3109
-
-
Sander, C.1
Schneider, R.2
-
67
-
-
0028512129
-
A stochastic model for the evolution of autocorrelated DNA sequences
-
and
-
Schoniger M., and von Haeseler A., 1994. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phylogenet Evol., 3: 240–7.
-
(1994)
Mol. Phylogenet Evol
, vol.3
, pp. 240-247
-
-
Schoniger, M.1
von Haeseler, A.2
-
68
-
-
0027952860
-
Compensating changes in protein multiple sequences alignments
-
and
-
Taylor W.R., and Hatrick K., 1994. Compensating changes in protein multiple sequences alignments. Protein Engineering, 7: 341–8.
-
(1994)
Protein Engineering
, vol.7
, pp. 341-348
-
-
Taylor, W.R.1
Hatrick, K.2
-
69
-
-
0037433701
-
Using multiple interdependency to separate functional from phylogentic correlations in protein alignments
-
and
-
Tillier E.R.M., and Lui T.W.H., 2003. Using multiple interdependency to separate functional from phylogentic correlations in protein alignments. Bioinformatics, 19: 750–5.
-
(2003)
Bioinformatics
, vol.19
, pp. 750-755
-
-
Tillier, E.R.M.1
Lui, T.W.H.2
-
70
-
-
33646822044
-
Codep: maximizing coevolutionary interdependencies to discover interacting proteins
-
and
-
Tillier E.R., Biro L., Li G., and Tillo D., 2006. Codep: maximizing coevolutionary interdependencies to discover interacting proteins. Proteins, 63: 822–31.
-
(2006)
Proteins
, vol.63
, pp. 822-831
-
-
Tillier, E.R.1
Biro, L.2
Li, G.3
Tillo, D.4
-
71
-
-
34047228912
-
Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses
-
and, Ahead publication
-
Travers S.A.A., and Fares M.A., 2007. Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. Mol. Biol. Evol., Ahead publication.
-
(2007)
Mol. Biol. Evol
-
-
Travers, S.A.A.1
Fares, M.A.2
-
72
-
-
13344260693
-
Coevolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides
-
and
-
Van Kesteren R.E., Tensen C.P., Smit A.B., van Minnen J., Kolakowski L.F., Meyerhof W., Richter D., van Heerikhuizen H., Vreugdenhil E., and Geraerts W.P., 1996. Coevolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides. J. Biol. Chem., 271: 3619–26.
-
(1996)
J. Biol. Chem
, vol.271
, pp. 3619-3626
-
-
Van Kesteren, R.E.1
Tensen, C.P.2
Smit, A.B.3
van Minnen, J.4
Kolakowski, L.F.5
Meyerhof, W.6
Richter, D.7
van Heerikhuizen, H.8
Vreugdenhil, E.9
Geraerts, W.P.10
-
73
-
-
41049092793
-
Phylogenetic methodology for detecting protein interactions
-
and, Ahead publication
-
Waddell P.J., Kishino H., and Ota R., 2006. Phylogenetic methodology for detecting protein interactions. Mol. Biol. Evol., Ahead publication.
-
(2006)
Mol. Biol. Evol
-
-
Waddell, P.J.1
Kishino, H.2
Ota, R.3
-
74
-
-
0042672578
-
Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information
-
and
-
Weckwerth W., and Selbig J., 2003. Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information. Biochemical and Biophysical Research Communications, 307: 516–21.
-
(2003)
Biochemical and Biophysical Research Communications
, vol.307
, pp. 516-521
-
-
Weckwerth, W.1
Selbig, J.2
-
75
-
-
0034724418
-
Separation of phylogentic and functional associations in biological sequences by using the parametric bootstrap
-
and
-
Wollenberg K.R., and Atchley W.R., 2000. Separation of phylogentic and functional associations in biological sequences by using the parametric bootstrap. Proc. Natl. Acad. Sci. U.S.A., 97: 3288–91.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 3288-3291
-
-
Wollenberg, K.R.1
Atchley, W.R.2
-
76
-
-
0033609902
-
Evolution of protein sequences and structures
-
and
-
Wood T.C., and Pearson W.R., 1999. Evolution of protein sequences and structures. J. Mol. Biol., 291: 977–95.
-
(1999)
J. Mol. Biol
, vol.291
, pp. 977-995
-
-
Wood, T.C.1
Pearson, W.R.2
-
77
-
-
0035986872
-
Functional pro, iscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormone
-
and
-
Yi S., Bernat B., Pal G., Kossiakoff A., and Li W.-H., 2002. Functional pro, iscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormone. Mol. Biol. Evol., 19: 1083–92.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 1083-1092
-
-
Yi, S.1
Bernat, B.2
Pal, G.3
Kossiakoff, A.4
Li, W.-H.5
-
78
-
-
33749514099
-
Genomic analysis of the hierarchical structure of regulatory networks
-
and
-
Yu H., and Gerstein M., 2006. Genomic analysis of the hierarchical structure of regulatory networks. Proc. Natl. Acad. Sci. U.S.A., 103: 14724–31.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.103
, pp. 14724-14731
-
-
Yu, H.1
Gerstein, M.2
-
79
-
-
0037057376
-
Genomic functional annotation using coevolution profiles of gene clusters
-
and, : research0060.1–0060.9
-
Zeng Y., Roberts R.J., and Kasif S., 2002. Genomic functional annotation using coevolution profiles of gene clusters. Genome Biology, 3: research0060.1–0060.9.
-
(2002)
Genome Biology
, vol.3
-
-
Zeng, Y.1
Roberts, R.J.2
Kasif, S.3
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