-
2
-
-
33845362968
-
Measuring covariation in RNA alignments: Physical realism improves information measures
-
17038338
-
Measuring covariation in RNA alignments: physical realism improves information measures. S Lindgreen PP Gardner A Krogh, Bioinformatics 2006 22 24 2988 2995 17038338
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 2988-2995
-
-
Lindgreen, S.1
Gardner, P.P.2
Krogh, A.3
-
3
-
-
34548457666
-
Detecting the coevolution of biosequences-an example of RNA interaction prediction
-
17636042
-
Detecting the coevolution of biosequences-an example of RNA interaction prediction. CH Yeang JFJ Darot HF Noller D Haussler, Mol Biol Evol 2007 24 9 2119 2131 17636042
-
(2007)
Mol Biol Evol
, vol.24
, Issue.9
, pp. 2119-2131
-
-
Yeang, C.H.1
Darot, J.F.J.2
Noller, H.F.3
Haussler, D.4
-
4
-
-
0028084754
-
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
-
8177884
-
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? IN Shindyalov NA Kolchanov C Sander, Protein Engineering 1994 7 3 349 358 8177884
-
(1994)
Protein Engineering
, vol.7
, Issue.3
, pp. 349-358
-
-
Shindyalov, I.N.1
Kolchanov, N.A.2
Sander, C.3
-
5
-
-
0033582946
-
Coevolving protein residues: Maximum likelihood identification and relationship to structure
-
10074416
-
Coevolving protein residues: maximum likelihood identification and relationship to structure. DD Pollock WR Taylor N Goldman, J Mol Biol 1999 287 187 198 10074416
-
(1999)
J Mol Biol
, vol.287
, pp. 187-198
-
-
Pollock, D.D.1
Taylor, W.R.2
Goldman, N.3
-
6
-
-
36949019322
-
Detecting coevolution in and among protein domains
-
17983264
-
Detecting coevolution in and among protein domains. CH Yeang D Haussler, PLoS Comput Biol 2007 3 11 e211 17983264
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.11
, pp. 211
-
-
Yeang, C.H.1
Haussler, D.2
-
7
-
-
36148966864
-
Coevolutionary patterns in cytochrome coxidase subunit I depend on structural and functional context
-
17955155
-
Coevolutionary patterns in cytochrome coxidase subunit I depend on structural and functional context. ZO Wang DD Pollock, J Mol Evol 2007 65 5 485 495 17955155
-
(2007)
J Mol Evol
, vol.65
, Issue.5
, pp. 485-495
-
-
Wang, Z.O.1
Pollock, D.D.2
-
8
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
9281423
-
Correlated mutations contain information about protein-protein interaction. F Pazos HM Citterich G Ausiello A Valencia, J Mol Biol 1997 271 4 511 523 9281423
-
(1997)
J Mol Biol
, vol.271
, Issue.4
, pp. 511-523
-
-
Pazos, F.1
Citterich, H.M.2
Ausiello, G.3
Valencia, A.4
-
9
-
-
0034724418
-
Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap
-
10725404
-
Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. KR Wollenberg WR Atchley, Proc Natl Acad Sci USA 2000 97 7 3288 3291 10725404
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.7
, pp. 3288-3291
-
-
Wollenberg, K.R.1
Atchley, W.R.2
-
10
-
-
0042767572
-
Using multiple sequence correlation analysis to characterize functionally important protein regions
-
12874372
-
Using multiple sequence correlation analysis to characterize functionally important protein regions. MC Saraf GL Moore CD Maranas, Protein Eng 2003 16 6 397 406 12874372
-
(2003)
Protein Eng
, vol.16
, Issue.6
, pp. 397-406
-
-
Saraf, M.C.1
Moore, G.L.2
Maranas, C.D.3
-
11
-
-
0033536602
-
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
-
10514373
-
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families. SW Lockless R Ranganathan, Science 1999 286 5438 295 299 10514373
-
(1999)
Science
, vol.286
, Issue.5438
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
12
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
12483203
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins. GM Suel SW Lockless MA Wall R Ranganathan, Nat Struct Biol 2003 10 59 69 12483203
-
(2003)
Nat Struct Biol
, vol.10
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
14
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
7984417
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 7984417
-
(1994)
Nucleic Acids Res
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
15
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
16332807
-
UniFrac: a new phylogenetic method for comparing microbial communities. C Lozupone R Knight, Appl Environ Microbiol 2005 71 12 8228 8235 16332807
-
(2005)
Appl Environ Microbiol
, vol.71
, Issue.12
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
16
-
-
33744829032
-
Inferring functional linkages between proteins from evolutionary scenarios
-
16674974
-
Inferring functional linkages between proteins from evolutionary scenarios. Y Zhou R Wang L Li X Xia Z Sun, J Mol Biol 2006 359 4 1150 1159 16674974
-
(2006)
J Mol Biol
, vol.359
, Issue.4
, pp. 1150-1159
-
-
Zhou, Y.1
Wang, R.2
Li, L.3
Xia, X.4
Sun, Z.5
-
17
-
-
0033744204
-
Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
-
11070062
-
Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. P Tuffery P Darlu, Mol Biol Evol 2000 17 11 1753 1759 11070062
-
(2000)
Mol Biol Evol
, vol.17
, Issue.11
, pp. 1753-1759
-
-
Tuffery, P.1
Darlu, P.2
-
18
-
-
55449127787
-
Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
-
16103904
-
Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. D Barker M Pagel, PLoS Comput Biol 2005 1 e3 16103904
-
(2005)
PLoS Comput Biol
, vol.1
, pp. 3
-
-
Barker, D.1
Pagel, M.2
-
19
-
-
84860533518
-
Detecting coevolving amino acid sites using Bayesian mutational mapping
-
15961449
-
Detecting coevolving amino acid sites using Bayesian mutational mapping. MW Dimmic MJ Hubisz CD Bustamante R Nielsen, Bioinformatics 2005 21 Suppl 1 i126 i135 15961449
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Dimmic, M.W.1
Hubisz, M.J.2
Bustamante, C.D.3
Nielsen, R.4
-
20
-
-
39649100613
-
Detecting groups of coevolving positions in a molecule: A clustering approach
-
18053141
-
Detecting groups of coevolving positions in a molecule: a clustering approach. J Dutheil N Galtier, BMC Evol Biol 2007 7 242 18053141
-
(2007)
BMC Evol Biol
, vol.7
, pp. 242
-
-
Dutheil, J.1
Galtier, N.2
-
21
-
-
27944458910
-
Using information theory to search for co-evolving residues in proteins
-
16159918
-
Using information theory to search for co-evolving residues in proteins. LC Martin GB Gloor SD Dunn LM Wahl, Bioinformatics 2005 21 22 4116 4124 16159918
-
(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
-
22
-
-
38849115223
-
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
-
18057019
-
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. SD Dunn LM Wahl GB Gloor, Bioinformatics 2008 24 3 333 340 18057019
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 333-340
-
-
Dunn, S.D.1
Wahl, L.M.2
Gloor, G.B.3
-
23
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
9278277
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. DD Pollock WR Taylor, Protein Eng 1997 10 6 647 657 9278277
-
(1997)
Protein Eng
, vol.10
, Issue.6
, pp. 647-657
-
-
Pollock, D.D.1
Taylor, W.R.2
-
24
-
-
23944476399
-
A model-based approach for detecting coevolving positions in a molecule
-
15944445
-
A model-based approach for detecting coevolving positions in a molecule. J Dutheil T Pupko A Jean-Marie N Galtier, Mol Biol Evol 2005 22 9 1919 1928 15944445
-
(2005)
Mol Biol Evol
, vol.22
, Issue.9
, pp. 1919-1928
-
-
Dutheil, J.1
Pupko, T.2
Jean-Marie, A.3
Galtier, N.4
-
25
-
-
0037433701
-
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
-
12691987
-
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. ER Tillier TW Lui, Bioinformatics 2003 19 6 750 755 12691987
-
(2003)
Bioinformatics
, vol.19
, Issue.6
, pp. 750-755
-
-
Tillier, E.R.1
Lui, T.W.2
-
26
-
-
60849108455
-
Novel techniques for detecting correlated evolution
-
Australian National University
-
Novel techniques for detecting correlated evolution. BC Easton, PhD thesis Australian National University 2006
-
(2006)
PhD Thesis
-
-
Easton, B.C.1
-
28
-
-
16544384596
-
Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs
-
15502829
-
Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. AD Kern FA Kondrashov, Nat Genet 2004 36 11 1207 12 15502829
-
(2004)
Nat Genet
, vol.36
, Issue.11
, pp. 1207-12
-
-
Kern, A.D.1
Kondrashov, F.A.2
-
29
-
-
3042842115
-
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
-
15211506
-
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. AA Fodor RW Aldrich, Proteins 2004 56 2 211 221 15211506
-
(2004)
Proteins
, vol.56
, Issue.2
, pp. 211-221
-
-
Fodor, A.A.1
Aldrich, R.W.2
-
30
-
-
2442498470
-
On evolutionary conservation of thermodynamic coupling in proteins
-
15023994
-
On evolutionary conservation of thermodynamic coupling in proteins. AA Fodor RW Aldrich, J Biol Chem 2004 279 18 19046 19050 15023994
-
(2004)
J Biol Chem
, vol.279
, Issue.18
, pp. 19046-19050
-
-
Fodor, A.A.1
Aldrich, R.W.2
-
31
-
-
19944406094
-
Context dependence and coevolution among amino acid residues in proteins
-
15865995
-
Context dependence and coevolution among amino acid residues in proteins. ZO Wang DD Pollock, Methods Enzymol 2005 395 779 790 15865995
-
(2005)
Methods Enzymol
, vol.395
, pp. 779-790
-
-
Wang, Z.O.1
Pollock, D.D.2
-
32
-
-
38049186804
-
Correlated substitution analysis and the prediction of amino acid structural contacts
-
18000015
-
Correlated substitution analysis and the prediction of amino acid structural contacts. DS Horner W Pirovano G Pesole, Brief Bioinform 2008 9 46 56 18000015
-
(2008)
Brief Bioinform
, vol.9
, pp. 46-56
-
-
Horner, D.S.1
Pirovano, W.2
Pesole, G.3
-
33
-
-
0023461350
-
Helix stabilization by Glu-.Lys+ salt bridges in short peptides of de novo design
-
3122208
-
Helix stabilization by Glu-.Lys+ salt bridges in short peptides of de novo design. S Marqusee RL Baldwin, Proc Natl Acad Sci USA 1987 84 24 8898 8902 3122208
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, Issue.24
, pp. 8898-8902
-
-
Marqusee, S.1
Baldwin, R.L.2
-
34
-
-
0025756736
-
Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles
-
2010920
-
Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles. L Serrano M Bycroft AR Fersht, J Mol Biol 1991 218 2 465 475 2010920
-
(1991)
J Mol Biol
, vol.218
, Issue.2
, pp. 465-475
-
-
Serrano, L.1
Bycroft, M.2
Fersht, A.R.3
-
35
-
-
0027475153
-
Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings
-
8443591
-
Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. BM Huyghues-Despointes JM Scholtz RL Baldwin, Protein Sci 1993 2 80 85 8443591
-
(1993)
Protein Sci
, vol.2
, pp. 80-85
-
-
Huyghues-Despointes, B.M.1
Scholtz, J.M.2
Baldwin, R.L.3
-
36
-
-
0028920304
-
Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: Effects on structure, stability and the binding of solvent
-
7869383
-
Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent. M Blaber WA Baase N Gassner BW Matthews, J Mol Biol 1995 246 2 317 330 7869383
-
(1995)
J Mol Biol
, vol.246
, Issue.2
, pp. 317-330
-
-
Blaber, M.1
Baase, W.A.2
Gassner, N.3
Matthews, B.W.4
-
37
-
-
0542406203
-
Stabilization of the long central helix of troponin C by intrahelical salt bridges between charged amino acid side chains
-
3865207
-
Stabilization of the long central helix of troponin C by intrahelical salt bridges between charged amino acid side chains. M Sundaralingam W Drendel M Greaser, Proc Natl Acad Sci USA 1985 82 23 7944 7947 3865207
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, Issue.23
, pp. 7944-7947
-
-
Sundaralingam, M.1
Drendel, W.2
Greaser, M.3
-
38
-
-
0027960477
-
Discovering structural correlations in alpha-helices
-
7849600
-
Discovering structural correlations in alpha-helices. TM Klingler DL Brutlag, Protein Sci 1994 3 10 1847 1857 7849600
-
(1994)
Protein Sci
, vol.3
, Issue.10
, pp. 1847-1857
-
-
Klingler, T.M.1
Brutlag, D.L.2
-
39
-
-
33747791711
-
Statistical analysis of intrahelical ionic interactions in alpha-helices and coiled coils
-
16876432
-
Statistical analysis of intrahelical ionic interactions in alpha-helices and coiled coils. M Meier P Burkhard, J Struct Biol 2006 155 2 116 129 16876432
-
(2006)
J Struct Biol
, vol.155
, Issue.2
, pp. 116-129
-
-
Meier, M.1
Burkhard, P.2
-
40
-
-
0032486233
-
Intrahelical side chain interactions in alpha-helices: Poor correlation between energetics and frequency
-
9657391
-
Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency. J Fernandez-Recio J Sancho, FEBS Lett 1998 429 99 103 9657391
-
(1998)
FEBS Lett
, vol.429
, pp. 99-103
-
-
Fernandez-Recio, J.1
Sancho, J.2
-
41
-
-
36949003878
-
Co-evolving residues in membrane proteins
-
18065429
-
Co-evolving residues in membrane proteins. A Fuchs AJ Martin-Galiano M Kalman S Fleishman N Ben-Tal D Frishman, Bioinformatics 2007 23 24 3312 3319 18065429
-
(2007)
Bioinformatics
, vol.23
, Issue.24
, pp. 3312-3319
-
-
Fuchs, A.1
Martin-Galiano, A.J.2
Kalman, M.3
Fleishman, S.4
Ben-Tal, N.5
Frishman, D.6
-
44
-
-
44849134159
-
Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations
-
18555187
-
Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations. M Buvoli M Hamady LA Leinwand R Knight, Trends Cardiovasc Med 2008 18 4 141 149 18555187
-
(2008)
Trends Cardiovasc Med
, vol.18
, Issue.4
, pp. 141-149
-
-
Buvoli, M.1
Hamady, M.2
Leinwand, L.A.3
Knight, R.4
-
45
-
-
34748893838
-
PyCogent: A toolkit for making sense from sequence
-
17708774
-
PyCogent: a toolkit for making sense from sequence. R Knight P Maxwell A Birmingham J Carnes JG Caporaso BC Easton M Eaton M Hamady H Lindsay Z Liu C Lozupone D McDonald M Robeson R Sammut S Smit MJ Wakefield J Widmann S Wikman S Wilson H Ying GA Huttley, Genome Biol 2007 8 8 R171 17708774
-
(2007)
Genome Biol
, vol.8
, Issue.8
, pp. 171
-
-
Knight, R.1
Maxwell, P.2
Birmingham, A.3
Carnes, J.4
Caporaso, J.G.5
Easton, B.C.6
Eaton, M.7
Hamady, M.8
Lindsay, H.9
Liu, Z.10
Lozupone, C.11
McDonald, D.12
Robeson, M.13
Sammut, R.14
Smit, S.15
Wakefield, M.J.16
Widmann, J.17
Wikman, S.18
Wilson, S.19
Ying, H.20
Huttley, G.A.21
more..
-
46
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
3447015
-
The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 4 406 425 3447015
-
(1987)
Mol Biol Evol
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
47
-
-
60849130233
-
-
W.H. Freeman and Company
-
RR Sokal FJ Rohlf, Biometry W.H. Freeman and Company 1997 chap 18 813 819
-
(1997)
Biometry
, vol.18
, pp. 813-819
-
-
Sokal, R.R.1
Rohlf, F.J.2
|