-
1
-
-
0033550256
-
Effective use of sequence correlation and conservation in fold recognition
-
Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:12211239.
-
(1999)
J Mol Biol
, vol.293
, pp. 12211239
-
-
Olmea, O.1
Rost, B.2
Valencia, A.3
-
2
-
-
0032613288
-
Ab initio folding of proteins using restraints derived from evolutionary information
-
DOI 10.1002/(SICI)1097-0134(1999)37:3+<177::AID-PROT22>3.0.CO;2-E
-
Ortiz AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins 1999;(Suppl 3):177-185. (Pubitemid 29463529)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.37
, Issue.SUPPL. 3
, pp. 177-185
-
-
Ortiz, A.R.1
Kolinski, A.2
Rotkiewicz, P.3
Ilkowski, B.4
Skolnick, J.5
-
3
-
-
21644454183
-
Scoring docking models with evolutionary information
-
DOI 10.1002/prot.20570
-
Tress M, de Juan D, Grana O, Gomez MJ, Gomez-Puertas P, Gonzalez JM., Lopez G, Valencia A. Scoring docking models with evolutionary information. Proteins 2005;60:275-280. (Pubitemid 40934899)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.60
, Issue.2
, pp. 275-280
-
-
Tress, M.1
De Juan, D.2
Grana, O.3
Gomez, M.J.4
Gomez-Puertas, P.5
Gonzalez, J.M.6
Lopez, G.7
Valencia, A.8
-
4
-
-
36949003878
-
Co-evolving residues in membrane proteins
-
Fuchs A, Martin-Galiano AJ, Kaiman M, Fleishman S, Ben-Tal N, Frishman D. Co-evolving residues in membrane proteins. Bioinformatics 2007;23:3312-3319.
-
(2007)
Bioinformatics
, vol.23
, pp. 3312-3319
-
-
Fuchs, A.1
Martin-Galiano, A.J.2
Kaiman, M.3
Fleishman, S.4
Ben-Tal, N.5
Frishman, D.6
-
5
-
-
0023660022
-
Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
-
Altschuh D, Lesk AM, Bloomer AC, Klug A. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 1987;193:693-707.
-
(1987)
J Mol Biol
, vol.193
, pp. 693-707
-
-
Altschuh, D.1
Lesk, A.M.2
Bloomer, A.C.3
Klug, A.4
-
6
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel U, Sander C, Schnieder R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317. (Pubitemid 24111530)
-
(1994)
Proteins: Structure, Function and Genetics
, vol.18
, Issue.4
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
7
-
-
0028125904
-
How frequent are correlated changes in families of protein sequences?
-
Neher E. How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci. USA 1994;91:98-102.
-
(1994)
Proc Natl Acad Sci. USA
, vol.91
, pp. 98-102
-
-
Neher, E.1
-
8
-
-
0028084754
-
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
-
Shindyalov IN, Kolchanov NA, Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 1994;7:349-358.
-
(1994)
Protein Eng
, vol.7
, pp. 349-358
-
-
Shindyalov, I.N.1
Kolchanov, N.A.2
Sander, C.3
-
9
-
-
0027952860
-
Compensating changes in protein multiple sequence alignments
-
Taylor WR, Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng 1994;7:341-348.
-
(1994)
Protein Eng
, vol.7
, pp. 341-348
-
-
Taylor, W.R.1
Hatrick, K.2
-
10
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996;257:342-358.
-
(1996)
J Mol Biol
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
11
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea I, Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des 1997;2:S25-S32.
-
(1997)
Fold des
, vol.2
-
-
Olmea, I.1
Valencia, A.2
-
12
-
-
0034721944
-
Analysis of co-variation in an SH3 domain, sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
-
Larson SM, Di Nardo AA, Davidson AR. Analysis of co-variation in an SH3 domain, sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol 2000;303:433-446.
-
(2000)
J Mol Biol
, vol.303
, pp. 433-446
-
-
Larson, S.M.1
Di Nardo, A.A.2
Davidson, A.R.3
-
13
-
-
0034794239
-
Evaluation of a novel method for the identification, of coevolving protein residues
-
Pritchard L, Bladon P, Mitchell JMO, Dufton MJ. Evaluation of a novel method for the identification, of coevolving protein residues. Protein Eng 2001;14:549-555.
-
(2001)
Protein Eng
, vol.14
, pp. 549-555
-
-
Pritchard, L.1
Bladon, P.2
Mitchell, J.M.O.3
Dufton, M.J.4
-
14
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos F, Helmer-Citterich M., Ausiello G, Valencia. A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997;271:511-523.
-
(1997)
J Mol Biol
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
Valencia, A.4
-
15
-
-
0036763251
-
Prediction of protein residue contacts with a PDB-derived likelihood matrix
-
Singer MS, Vriend G, Bywater RP. Prediction of protein residue contacts with a PDB-derived likelihood matrix, Protein Eng 2002;15:721-725.
-
(2002)
Protein Eng
, vol.15
, pp. 721-725
-
-
Singer, M.S.1
Vriend, G.2
Bywater, R.P.3
-
16
-
-
0037433701
-
Using multiple inter-dependency to separate functional from phylogenetic correlations in protein alignments
-
Tillier ERM, Lui T. Using multiple inter-dependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics 2003;19:750-755.
-
(2003)
Bioinformatics
, vol.19
, pp. 750-755
-
-
Tillier, E.R.M.1
Lui, T.2
-
17
-
-
25444527443
-
Improved prediction of critical residues for protein function based on network and phylogenetic analyses
-
DOI 10.1186/1471-2105-6-213
-
Thibert B, Bredesen DE, del Rio D. Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics 2005:6:213. (Pubitemid 41372453)
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 213
-
-
Thibert, B.1
Bredesen, D.E.2
Del Rio, G.3
-
18
-
-
27944458910
-
Using information theory to search for co-evolving residues in proteins
-
Martin LC, Gloor GB, Dunn SD, Wahl LM. Using information theory to search for co-evolving residues in proteins. Bioinformatics 2005;21:4116-4124.
-
(2005)
Bioinformatics
, vol.21
, pp. 4116-4124
-
-
Martin, L.C.1
Gloor, G.B.2
Dunn, S.D.3
Wahl, L.M.4
-
19
-
-
20844452182
-
Detection and reduction of evolutionary noise in correlated mutation analysis
-
Noivirt O, Eisenstein M, Horovitz A, Detection and reduction of evolutionary noise in correlated mutation analysis. Protein Eng Des Sel 2005;18:247-253.
-
(2005)
Protein Eng des Sel
, vol.18
, pp. 247-253
-
-
Noivirt, O.1
Eisenstein, M.2
Horovitz, A.3
-
20
-
-
38049186804
-
Correlated substitution analysis and the prediction of amino acid structural contacts
-
Horner DS, Pirovano W, Pesote G. Correlated substitution analysis and the prediction of amino acid structural contacts. Briefings Bioinform 2008;9:46-56.
-
(2008)
Briefings Bioinform
, vol.9
, pp. 46-56
-
-
Horner, D.S.1
Pirovano, W.2
Pesote, G.3
-
21
-
-
39149083126
-
Predicting disulfide bond connectivity in proteins by correlated mutations analysis
-
Rubenstein R, Fiser A. Predicting disulfide bond connectivity in proteins by correlated mutations analysis. Bioinformatics 2008;24:498-504.
-
(2008)
Bioinformatics
, vol.24
, pp. 498-504
-
-
Rubenstein, R.1
Fiser, A.2
-
22
-
-
38849115223
-
Mutual Information without the influence of phylogeny or entropy dramatically improve residue contact prediction
-
Dunn SD, Wahl LM, Gloor GB. Mutual Information without the influence of phylogeny or entropy dramatically improve residue contact prediction. Bioinformatics 2008;24:333-340.
-
(2008)
Bioinformatics
, vol.24
, pp. 333-340
-
-
Dunn, S.D.1
Wahl, L.M.2
Gloor, G.B.3
-
23
-
-
59849106575
-
Optimal data collection for correlated mutation analysis
-
Ashkenanzy H, Unger R, Kliger Y. Optimal data collection for correlated mutation analysis. Proteins 2009;74:545-555.
-
(2009)
Proteins
, vol.74
, pp. 545-555
-
-
Ashkenanzy, H.1
Unger, R.2
Kliger, Y.3
-
25
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
Pollock DD, Taylor WR. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng 1997;10:647-657.
-
(1997)
Protein Eng
, vol.10
, pp. 647-657
-
-
Pollock, D.D.1
Taylor, W.R.2
-
26
-
-
0033744204
-
Exploring an phylogenetic approach for the detection of correlated substitutions in proteins
-
Tuffery P, Darlu P. Exploring an phylogenetic approach for the detection of correlated substitutions in proteins. Mol Biol Evol 2000;17:1753-1759.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 1753-1759
-
-
Tuffery, P.1
Darlu, P.2
-
27
-
-
0033977832
-
Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis
-
Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol 2000;17:164-178.
-
(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
-
28
-
-
33751017993
-
CAPS: Coevolution analysis using protein sequences
-
Fares MA, McNally D. CAPS: coevolution analysis using protein sequences. Bioinformatics 2006;22:2821-2822.
-
(2006)
Bioinformatics
, vol.22
, pp. 2821-2822
-
-
Fares, M.A.1
McNally, D.2
-
29
-
-
43649101406
-
Reducing the false positive rate in the non-parametric analysis of molecular coevolution
-
Codoñer FM., O'Dea S, Fares MA. Reducing the false positive rate in the non-parametric analysis of molecular coevolution. BMC Evol Biol 2008:8:106.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 106
-
-
Codoñer, F.M.1
O'Dea, S.2
Fares, M.A.3
-
30
-
-
4043170491
-
Protein contact, prediction using patterns of correlation
-
Hamilton. N, Burrage K, Ragan. MA, Huber T. Protein contact, prediction using patterns of correlation. Proteins 2004;56:679684.
-
(2004)
Proteins
, vol.56
, pp. 679684
-
-
Hamilton, N.1
Burrage, K.2
Ragan, M.A.3
Huber, T.4
-
32
-
-
0034213559
-
Conservation of polar residues as hot spots at protein interfaces
-
Hu Z, Ma B, Woifson H, Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins 2000;39:331342.
-
(2000)
Proteins
, vol.39
, pp. 331342
-
-
Hu, Z.1
Ma, B.2
Woifson, H.3
Nussinov, R.4
-
33
-
-
0035838976
-
Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
-
DOI 10.1006/jmbi.2001.4870
-
Aloy P, Querol E, Aviles FX, Sternberg MJ. Automated structurebased prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 2001;311:395-408. (Pubitemid 32744549)
-
(2001)
Journal of Molecular Biology
, vol.311
, Issue.2
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.X.3
Sternberg, M.J.E.4
-
34
-
-
18544362952
-
Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions
-
Gloor GB, Martin LC, Wahl LM, Dunn SD. Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. Biochemistry 2005;44:7156-7165.
-
(2005)
Biochemistry
, vol.44
, pp. 7156-7165
-
-
Gloor, G.B.1
Martin, L.C.2
Wahl, L.M.3
Dunn, S.D.4
-
35
-
-
40749144489
-
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
-
Manning JR, Jefferson ER, Barton GJ. The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics 2008;9:51-66.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 51-66
-
-
Manning, J.R.1
Jefferson, E.R.2
Barton, G.J.3
-
37
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A. Pfam: clans, web tools and services. Nucleic Acid Res 2006;34:D247-D251.
-
(2006)
Nucleic Acid Res
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Böckler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.L.12
Bateman, A.13
-
38
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22:1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
39
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Wessig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Wessig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
40
-
-
84856043672
-
A mathematical theory of communication
-
Shannon CE. A mathematical theory of communication. Bell Syst Tech. J. 1948;27:379-423.
-
(1948)
Bell Syst Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
41
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff J. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:1091510919.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 1091510919
-
-
Henikoff, S.1
Henikoff, J.2
-
42
-
-
0242490780
-
Cytoscape: A software enviroment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang TJ, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software enviroment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-2504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, T.J.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
43
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoč 2007;2:23662382.
-
(2007)
Nat Protoč
, vol.2
, pp. 23662382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
Workman, C.6
Christmas, R.7
Avila-Campilo, I.8
Creech, M.9
Gross, B.10
Hanspers, K.11
Isserlin, R.12
Kelley, R.13
Killcoyne, S.14
Lotia, S.15
Maere, S.16
Morris, J.17
Ono, K.18
Pavlovic, V.19
Pico, A.R.20
Vailaya, A.21
Wang, P.L.22
Adler, A.23
Conklin, B.R.24
Hood, L.25
Kuiper, M.26
Sander, C.27
Schmulevich, I.28
Schwikowski, B.29
Warner, G.J.30
Ideker, T.31
Bader, G.D.32
more..
-
44
-
-
3042842115
-
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
-
Fodor AA, Aldrich RW. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 2004;56:211-221.
-
(2004)
Proteins
, vol.56
, pp. 211-221
-
-
Fodor, A.A.1
Aldrich, R.W.2
-
45
-
-
33646766064
-
Correlated mutations: Advances and limitations. A study on fusion proteins and on the CohesinDockerin families
-
Halperin I, Wolfson H, Nussinov R. Correlated mutations: advances and limitations. A study on fusion proteins and on the CohesinDockerin families. Proteins 2006;63:832-845.
-
(2006)
Proteins
, vol.63
, pp. 832-845
-
-
Halperin, I.1
Wolfson, H.2
Nussinov, R.3
|