-
1
-
-
0033977832
-
Correlations among amino acid sites in bBLH protein domains: An information theoretic analysis
-
Atchley, W.R., Wollenberg, K.R., Fitch, W.M., Terhalle, W. and Dress, A.W. 2000. Correlations among amino acid sites in bBLH 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
-
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
-
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.SUPPL. 1
-
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
, Issue.I126-35
-
-
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
-
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
-
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
-
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
-
-
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.
-
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.
-
-
-
-
24
-
-
3042842115
-
-
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.
-
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.
-
-
-
-
25
-
-
2942695714
-
Coevolution of gene expression among interacting proteins
-
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. USA., 101:9033-8.
-
(2004)
Proc. Natl. Acad. Sci. USA
, 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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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)
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
, Issue.I328-37
-
-
Nimrod, G.1
Glaser, F.2
Steinberg, D.3
Ben-Tal, N.4
Pupko, T.5
-
52
-
-
0037020282
-
Correlated mutation apalyses on very large sequence families
-
Olivera, L., Paiva, A.C.M and Vriend, G. 2002. Correlated mutation apalyses 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
-
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
-
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
-
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
-
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
-
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 sequeces using log-likelihood ratios
-
Pei, J., Cai, W., Kinc, L.N. and Grishin, N.V. 2006. Prediction of functional specificity determinants from protein sequeces 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 furietions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. and Yeates, T.O. 1999. Assigning protein furietions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA., 96:4285-8.
-
(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
-
61
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|