-
1
-
-
84867605737
-
Accurate simulation and detection of coevolution signals in multiple sequence alignments
-
Ackerman SH, Tillier ER, Gatti DL. 2012. Accurate simulation and detection of coevolution signals in multiple sequence alignments. PLoS One 7(10):e47108.
-
(2012)
PLoS One
, vol.7
, Issue.10
, pp. e47108
-
-
Ackerman, S.H.1
Tillier, E.R.2
Gatti, D.L.3
-
2
-
-
84874079397
-
Using analyses of amino acid coevolution to understand protein structure and function
-
Ashenberg O, Laub MT. 2013. Using analyses of amino acid coevolution to understand protein structure and function. Methods Enzymol. 523:191-212.
-
(2013)
Methods Enzymol.
, vol.523
, pp. 191-212
-
-
Ashenberg, O.1
Laub, M.T.2
-
3
-
-
0033977832
-
Correlations among amino acid sites in bhlh protein domains: An information theoretic analysis
-
Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW. 2000. Correlations among amino acid sites in bhlh protein domains: an information theoretic analysis. Mol Biol Evol. 17(1):164-178.
-
(2000)
Mol Biol Evol.
, vol.17
, Issue.1
, pp. 164-178
-
-
Atchley, W.R.1
Wollenberg, K.R.2
Fitch, W.M.3
Terhalle, W.4
Dress, A.W.5
-
4
-
-
0036435882
-
Analysis of catalytic residues in enzyme active sites
-
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM. 2002. Analysis of catalytic residues in enzyme active sites. J Mol Biol. 324(1):105-121.
-
(2002)
J Mol Biol.
, vol.324
, Issue.1
, pp. 105-121
-
-
Bartlett, G.J.1
Porter, C.T.2
Borkakoti, N.3
Thornton, J.M.4
-
5
-
-
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(6):e10779.
-
(2010)
PLoS One
, vol.5
, Issue.6
, pp. e10779
-
-
Brown, C.A.1
Brown, K.S.2
-
6
-
-
78649704332
-
Systematic dissection and trajectory-scanning mutagenesis of the molecular interface that ensures specificity of two-component signaling pathways
-
Capra EJ, Perchuk BS, Lubin EA, Ashenberg O, Skerker JM, Laub MT. 2010. Systematic dissection and trajectory-scanning mutagenesis of the molecular interface that ensures specificity of two-component signaling pathways. PLoS Genet. 6(11):e1001220.
-
(2010)
PLoS Genet.
, vol.6
, Issue.11
, pp. e1001220
-
-
Capra, E.J.1
Perchuk, B.S.2
Lubin, E.A.3
Ashenberg, O.4
Skerker, J.M.5
Laub, M.T.6
-
7
-
-
3543089710
-
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
-
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(10):1565-1572.
-
(2004)
Bioinformatics
, vol.20
, Issue.10
, pp. 1565-1572
-
-
Dekker, J.P.1
Fodor, A.2
Aldrich, R.W.3
Yellen, G.4
-
8
-
-
84902775598
-
Empirical fitness landscapes and the predictability of evolution
-
deVisser JAGM, Krug J. 2014. Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet. 15(7):480-490.
-
(2014)
Nat Rev Genet.
, vol.15
, Issue.7
, pp. 480-490
-
-
DeVisser, J.A.G.M.1
Krug, J.2
-
9
-
-
38849115223
-
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
-
Dunn SD, Wahl LM, Gloor GB. 2008. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24(3):333-340.
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 333-340
-
-
Dunn, S.D.1
Wahl, L.M.2
Gloor, G.B.3
-
10
-
-
84874041859
-
Protein engineering and stabilization from sequence statistics: Variation and covariation analysis
-
Durani V, Magliery TJ. 2013. Protein engineering and stabilization from sequence statistics: variation and covariation analysis. Methods Enzymol. 523:237-256.
-
(2013)
Methods Enzymol.
, vol.523
, pp. 237-256
-
-
Durani, V.1
Magliery, T.J.2
-
11
-
-
39649100613
-
Detecting groups of coevolving positions in a molecule: A clustering approach
-
Dutheil J, Galtier N. 2007. Detecting groups of coevolving positions in a molecule: a clustering approach. BMC Evol Biol. 7:242.
-
(2007)
BMC Evol Biol.
, vol.7
, pp. 242
-
-
Dutheil, J.1
Galtier, N.2
-
12
-
-
23944476399
-
A model-based approach for detecting coevolving positions in a molecule
-
Dutheil J, Pupko T, Jean-Marie A, Galtier N. 2005. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol. 22(9):1919-1928.
-
(2005)
Mol Biol Evol.
, vol.22
, Issue.9
, pp. 1919-1928
-
-
Dutheil, J.1
Pupko, T.2
Jean-Marie, A.3
Galtier, N.4
-
13
-
-
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(5):1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
14
-
-
0014860857
-
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
-
Fitch WM, 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 Genet. 4(5):579-593.
-
(1970)
Biochem Genet.
, vol.4
, Issue.5
, pp. 579-593
-
-
Fitch, W.M.1
Markowitz, E.2
-
15
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Göbel U, Sander C, Schneider R, Valencia A. 1994. Correlated mutations and residue contacts in proteins. Proteins 18(4):309-317.
-
(1994)
Proteins
, vol.18
, Issue.4
, pp. 309-317
-
-
Göbel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
16
-
-
0025675724
-
A maximum likelihood approach to the detection of selection from a phylogeny
-
Golding B, Felsenstein J. 1990. A maximum likelihood approach to the detection of selection from a phylogeny. J Mol Evol. 31(6):511-523.
-
(1990)
J Mol Evol.
, vol.31
, Issue.6
, pp. 511-523
-
-
Golding, B.1
Felsenstein, J.2
-
18
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52(5):696-704.
-
(2003)
Syst Biol.
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
19
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
-
Halpern AL, Bruno WJ. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol Biol Evol. 15(7):910-917.
-
(1998)
Mol Biol Evol.
, vol.15
, Issue.7
, pp. 910-917
-
-
Halpern, A.L.1
Bruno, W.J.2
-
20
-
-
84923079683
-
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors
-
Hopf TA, Morinaga S, Ihara S, Touhara K, Marks DS, Benton R. 2015. Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors. Nat Commun. 6:6077.
-
(2015)
Nat Commun.
, vol.6
, pp. 6077
-
-
Hopf, T.A.1
Morinaga, S.2
Ihara, S.3
Touhara, K.4
Marks, D.S.5
Benton, R.6
-
21
-
-
0036857358
-
Quicktree: Building huge neighbour-joining trees of protein sequences
-
Howe K, Bateman A, Durbin R. 2002. Quicktree: building huge neighbour-joining trees of protein sequences. Bioinformatics 18(11):1546-1547.
-
(2002)
Bioinformatics
, vol.18
, Issue.11
, pp. 1546-1547
-
-
Howe, K.1
Bateman, A.2
Durbin, R.3
-
22
-
-
83255165385
-
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees
-
Izquierdo-Carrasco F, Smith SA, Stamatakis A. 2011. Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinformatics 12:470.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 470
-
-
Izquierdo-Carrasco, F.1
Smith, S.A.2
Stamatakis, A.3
-
23
-
-
84856090271
-
Psicov: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones DT, Buchan DWA, Cozzetto D, Pontil M. 2012. Psicov: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2):184-190.
-
(2012)
Bioinformatics
, vol.28
, Issue.2
, pp. 184-190
-
-
Jones, D.T.1
Dwa, B.2
Cozzetto, D.3
Pontil, M.4
-
24
-
-
84884603324
-
Assessing the utility of co-evolution-based residue-residue contact predictions in a sequence-and structure-rich era
-
Kamisetty H, Ovchinnikov S, Baker D. 2013. Assessing the utility of co-evolution-based residue-residue contact predictions in a sequence-and structure-rich era. Proc Natl Acad Sci USA. 110(39):15674-15679.
-
(2013)
Proc Natl Acad Sci USA.
, vol.110
, Issue.39
, pp. 15674-15679
-
-
Kamisetty, H.1
Ovchinnikov, S.2
Baker, D.3
-
25
-
-
0000800333
-
On the probability of fixation of mutant genes in a population
-
Kimura M. 1962. On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
-
(1962)
Genetics
, vol.47
, pp. 713-719
-
-
Kimura, M.1
-
26
-
-
0027297096
-
Covariation of mutations in the v3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
-
Korber BT, Farber RM, Wolpert DH, Lapedes AS. 1993. Covariation of mutations in the v3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc Natl Acad Sci USA. 90(15):7176-7180.
-
(1993)
Proc Natl Acad Sci USA.
, vol.90
, Issue.15
, pp. 7176-7180
-
-
Korber, B.T.1
Farber, R.M.2
Wolpert, D.H.3
Lapedes, A.S.4
-
27
-
-
0034721944
-
Analysis of covariation in an sh3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
-
Larson SM, DiNardo AA, Davidson AR. 2000. Analysis of covariation in an sh3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol. 303(3):433-446.
-
(2000)
J Mol Biol.
, vol.303
, Issue.3
, pp. 433-446
-
-
Larson, S.M.1
DiNardo, A.A.2
Davidson, A.R.3
-
28
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless SW, Ranganathan R. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286(5438):295-299.
-
(1999)
Science
, vol.286
, Issue.5438
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
29
-
-
82855163967
-
Protein 3d structure computed from evolutionary sequence variation
-
Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. 2011. Protein 3d structure computed from evolutionary sequence variation. PLoS One 6(12):e28766.
-
(2011)
PLoS One
, vol.6
, Issue.12
, pp. e28766
-
-
Marks, D.S.1
Colwell, L.J.2
Sheridan, R.3
Hopf, T.A.4
Pagnani, A.5
Zecchina, R.6
Sander, C.7
-
30
-
-
27944458910
-
Using information theory to search for co-evolving residues in proteins
-
Martin LC, Gloor GB, Dunn SD, Wahl LM. 2005. Using information theory to search for co-evolving residues in proteins. Bioinformatics 21(22):4116-4124.
-
(2005)
Bioinformatics
, vol.21
, Issue.22
, pp. 4116-4124
-
-
Martin, L.C.1
Gloor, G.B.2
Dunn, S.D.3
Wahl, L.M.4
-
31
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z. 2005. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA. 102(31):10930-10935.
-
(2005)
Proc Natl Acad Sci USA.
, vol.102
, Issue.31
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
32
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. 2011. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci USA. 108(49):E1293-E1301.
-
(2011)
Proc Natl Acad Sci USA.
, vol.108
, Issue.49
, pp. E1293-E1301
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
Zecchina, R.7
Onuchic, J.N.8
Hwa, T.9
Weigt, M.10
-
33
-
-
84899847547
-
Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
-
Ovchinnikov S, Kamisetty H, Baker D. 2014. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife 3:e02030.
-
(2014)
Elife
, vol.3
, pp. e02030
-
-
Ovchinnikov, S.1
Kamisetty, H.2
Baker, D.3
-
34
-
-
77954270711
-
Guidance: A web server for assessing alignment confidence scores
-
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. 2010. Guidance: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38(Web Server issue):W23-W28.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W23-W28
-
-
Penn, O.1
Privman, E.2
Ashkenazy, H.3
Landan, G.4
Graur, D.5
Pupko, T.6
-
35
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
Pollock DD, Taylor WR. 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10(6):647-657.
-
(1997)
Protein Eng.
, vol.10
, Issue.6
, pp. 647-657
-
-
Pollock, D.D.1
Taylor, W.R.2
-
36
-
-
0033582946
-
Coevolving protein residues: Maximum likelihood identification and relationship to structure
-
Pollock DD, Taylor WR, Goldman N. 1999. Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol. 287(1):187-198.
-
(1999)
J Mol Biol.
, vol.287
, Issue.1
, pp. 187-198
-
-
Pollock, D.D.1
Taylor, W.R.2
Goldman, N.3
-
37
-
-
84455167671
-
Hot spots for allo-steric regulation on protein surfaces
-
Reynolds KA, McLaughlin RN, Ranganathan R. 2011. Hot spots for allo-steric regulation on protein surfaces. Cell 147(7):1564-1575.
-
(2011)
Cell
, vol.147
, Issue.7
, pp. 1564-1575
-
-
Reynolds, K.A.1
McLaughlin, R.N.2
Ranganathan, R.3
-
39
-
-
84879158202
-
Prediction of contacts from correlated sequence substitutions
-
Taylor WR, Hamilton RS, Sadowski MI. 2013. Prediction of contacts from correlated sequence substitutions. Curr Opin Struct Biol. 23(3):473-479.
-
(2013)
Curr Opin Struct Biol.
, vol.23
, Issue.3
, pp. 473-479
-
-
Taylor, W.R.1
Hamilton, R.S.2
Sadowski, M.I.3
-
40
-
-
84863393203
-
Protein topology from predicted residue contacts
-
Taylor WR, Jones DT, Sadowski MI. 2012. Protein topology from predicted residue contacts. Protein Sci. 21(2):299-305.
-
(2012)
Protein Sci.
, vol.21
, Issue.2
, pp. 299-305
-
-
Taylor, W.R.1
Jones, D.T.2
Sadowski, M.I.3
-
41
-
-
0037433701
-
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
-
Tillier ERM, Lui TWH. 2003. Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics 19(6):750-755.
-
(2003)
Bioinformatics
, vol.19
, Issue.6
, pp. 750-755
-
-
Erm, T.1
Lui, T.W.H.2
-
42
-
-
84925137444
-
Epistasis constrains mutational pathways of hemoglobin adaptation in high-altitude pikas
-
Tufts DM, Natarajan C, Revsbech IG, Projecto-Garcia J, Hoffmann FG, Weber RE, Fago A, Moriyama H, Storz JF. 2015. Epistasis constrains mutational pathways of hemoglobin adaptation in high-altitude pikas. Mol Biol Evol. 32(2):287-298.
-
(2015)
Mol Biol Evol.
, vol.32
, Issue.2
, pp. 287-298
-
-
Tufts, D.M.1
Natarajan, C.2
Revsbech, I.G.3
Projecto-Garcia, J.4
Hoffmann, F.G.5
Weber, R.E.6
Fago, A.7
Moriyama, H.8
Storz, J.F.9
-
43
-
-
59949096873
-
Ensemblcompara genetrees: Complete, duplication-aware phyloge-netic trees in vertebrates
-
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. 2009. Ensemblcompara genetrees: complete, duplication-aware phyloge-netic trees in vertebrates. Genome Res. 19(2):327-335.
-
(2009)
Genome Res.
, vol.19
, Issue.2
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
Birney, E.6
-
44
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich DM, Delaney NF, Depristo MA, Hartl DL. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312(5770):111-114.
-
(2006)
Science
, vol.312
, Issue.5770
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Ma, D.3
Hartl, D.L.4
-
45
-
-
4644373240
-
Estimating the frequency of events that cause multiple-nucleotide changes
-
Whelan S, Goldman N. 2004. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics 167(4): 2027-2043.
-
(2004)
Genetics
, vol.167
, Issue.4
, pp. 2027-2043
-
-
Whelan, S.1
Goldman, N.2
-
46
-
-
0034724418
-
Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap
-
Wollenberg KR, Atchley WR. 2000. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc Natl Acad Sci USA. 97(7): 3288-3291.
-
(2000)
Proc Natl Acad Sci USA.
, vol.97
, Issue.7
, pp. 3288-3291
-
-
Wollenberg, K.R.1
Atchley, W.R.2
-
48
-
-
36949019322
-
Detecting coevolution in and among protein domains
-
Yeang C-H, Haussler D. 2007. Detecting coevolution in and among protein domains. PLoS Comput Biol. 3(11):e211.
-
(2007)
PLoS Comput Biol.
, vol.3
, Issue.11
, pp. e211
-
-
Yeang, C.-H.1
Haussler, D.2
-
49
-
-
0023660653
-
Prediction of protein secondary structure and active sites using the alignment of homologous sequences
-
Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJ. 1987. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol. 195(4):957-961.
-
(1987)
J Mol Biol.
, vol.195
, Issue.4
, pp. 957-961
-
-
Zvelebil, M.J.1
Barton, G.J.2
Taylor, W.R.3
Sternberg, M.J.4
|