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Volumn 8, Issue , 2007, Pages

Supervised multivariate analysis of sequence groups to identify specificity determining residues

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENT SUBSTRATES; ENCODING SCHEMES; FUNCTIONAL CLASS; GROUP ANALYSIS; MULTI VARIATE ANALYSIS; MULTIPLE SEQUENCE ALIGNMENTS; MULTIVARIATE STATISTICAL METHOD; SERINE PROTEASE;

EID: 34249794262     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-135     Document Type: Article
Times cited : (24)

References (42)
  • 1
    • 0028871447 scopus 로고
    • Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering
    • 40667 7479856 10.1073/pnas.92.23.10639
    • Yuan L Voelker TA Hawkins DJ Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering Proc Natl Acad Sci U S A 1995 92 23 10639-10643 40667 7479856 10.1073/ pnas.92.23.10639
    • (1995) Proc Natl Acad Sci U S A , vol.92 , Issue.23 , pp. 10639-10643
    • Yuan, L.1    Voelker, T.A.2    Hawkins, D.J.3
  • 2
    • 0037470597 scopus 로고    scopus 로고
    • Automatic methods for predicting functionally important residues
    • 10.1016/S0022-2836(02)01451-1 12589769
    • del Sol Mesa A Pazos F Valencia A Automatic methods for predicting functionally important residues J Mol Biol 2003 326 4 1289-1302 10.1016/ S0022-2836(02)01451-1 12589769
    • (2003) J Mol Biol , vol.326 , Issue.4 , pp. 1289-1302
    • del Sol Mesa, A.1    Pazos, F.2    Valencia, A.3
  • 3
    • 0036205440 scopus 로고    scopus 로고
    • DIVERGE: Phylogeny-based analysis for functional-structural divergence of a protein family
    • 10.1093/bioinformatics/18.3.500 11934757
    • Gu X Vander Velden K DIVERGE: Phylogeny-based analysis for functional-structural divergence of a protein family Bioinformatics 2002 18 3 500-501 10.1093/bioinformatics/18.3.500 11934757
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 500-501
    • Gu, X.1    Vander Velden, K.2
  • 4
    • 27944461066 scopus 로고    scopus 로고
    • BADASP: Predicting functional specificity in protein families using ancestral sequences
    • 10.1093/bioinformatics/bti678 16159912
    • Edwards RJ Shields DC BADASP: Predicting functional specificity in protein families using ancestral sequences Bioinformatics 2005 21 22 4190-4191 10.1093/bioinformatics/bti678 16159912
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4190-4191
    • Edwards, R.J.1    Shields, D.C.2
  • 5
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • 10.1006/jmbi.1996.0167 8609628
    • Lichtarge O Bourne HR Cohen FE An evolutionary trace method defines binding surfaces common to protein families J Mol Biol 1996 257 2 342-358 10.1006/jmbi.1996.0167 8609628
    • (1996) J Mol Biol , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 6
    • 33748267918 scopus 로고    scopus 로고
    • Rank information: A structure-independent measure of evolutionary trace quality that improves identification of protein functional sites
    • 10.1002/prot.21101 16894615
    • Yao H Mihalek I Lichtarge O Rank information: A structure-independent measure of evolutionary trace quality that improves identification of protein functional sites Proteins 2006 65 1 111-123 10.1002/prot.21101 16894615
    • (2006) Proteins , vol.65 , Issue.1 , pp. 111-123
    • Yao, H.1    Mihalek, I.2    Lichtarge, O.3
  • 7
    • 33747840720 scopus 로고    scopus 로고
    • ET viewer: An application for predicting and visualizing functional sites in protein structures
    • 10.1093/bioinformatics/btl285 16809388
    • Morgan DH Kristensen DM Mittelman D Lichtarge O ET viewer: An application for predicting and visualizing functional sites in protein structures Bioinformatics 2006 22 16 2049-2050 10.1093/bioinformatics/ btl285 16809388
    • (2006) Bioinformatics , vol.22 , Issue.16 , pp. 2049-2050
    • Morgan, D.H.1    Kristensen, D.M.2    Mittelman, D.3    Lichtarge, O.4
  • 8
    • 0034644783 scopus 로고    scopus 로고
    • Analysis and prediction of functional sub-types from protein sequence alignments
    • 10.1006/jmbi.2000.4036 11021970
    • Hannenhalli SS Russell RB Analysis and prediction of functional sub-types from protein sequence alignments J Mol Biol 2000 303 1 61-76 10.1006/jmbi.2000.4036 11021970
    • (2000) J Mol Biol , vol.303 , Issue.1 , pp. 61-76
    • Hannenhalli, S.S.1    Russell, R.B.2
  • 9
    • 0027764344 scopus 로고
    • Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
    • 8143162
    • Livingstone CD Barton GJ Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation Comput Appl Biosci 1993 9 6 745-756 8143162
    • (1993) Comput Appl Biosci , vol.9 , Issue.6 , pp. 745-756
    • Livingstone, C.D.1    Barton, G.J.2
  • 10
    • 29144504098 scopus 로고    scopus 로고
    • Linking enzyme sequence to function using Conserved Property Difference Locator to identify and annotate positions likely to control specific functionality
    • 1326233 16318626 10.1186/1471-2105-6-284
    • Mayer KM McCorkle SR Shanklin J Linking enzyme sequence to function using Conserved Property Difference Locator to identify and annotate positions likely to control specific functionality BMC Bioinformatics 2005 6 284 1326233 16318626 10.1186/1471-2105-6-284
    • (2005) BMC Bioinformatics , vol.6 , pp. 284
    • Mayer, K.M.1    McCorkle, S.R.2    Shanklin, J.3
  • 11
    • 84886755836 scopus 로고    scopus 로고
    • CPDL Webserver http://genome.bnl.gov/CPDL/
  • 12
    • 0036352010 scopus 로고    scopus 로고
    • Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
    • 10.1016/S0022-2836(02)00587-9 12139929
    • Mirny LA Gelfand MS Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors J Mol Biol 2002 321 1 7-20 10.1016/S0022-2836(02)00587-9 12139929
    • (2002) J Mol Biol , vol.321 , Issue.1 , pp. 7-20
    • Mirny, L.A.1    Gelfand, M.S.2
  • 13
    • 1642452921 scopus 로고    scopus 로고
    • Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families
    • 10.1110/ps.03191704 14739328
    • Kalinina OV Mironov AA Gelfand MS Rakhmaninova AB Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families Protein Sci 2004 13 2 443-456 10.1110/ps.03191704 14739328
    • (2004) Protein Sci , vol.13 , Issue.2 , pp. 443-456
    • Kalinina, O.V.1    Mironov, A.A.2    Gelfand, M.S.3    Rakhmaninova, A.B.4
  • 14
    • 33845882991 scopus 로고    scopus 로고
    • Sequence comparison by sequence harmony identifies subtype-specific functional sites
    • 1702503 17130172
    • Pirovano W Feenstra KA Heringa J Sequence comparison by sequence harmony identifies subtype-specific functional sites Nucleic Acids Res 2006 1702503 17130172
    • (2006) Nucleic Acids Res
    • Pirovano, W.1    Feenstra, K.A.2    Heringa, J.3
  • 15
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • 332411 2172928 10.1093/nar/18.20.6097
    • Schneider TD Stephens RM Sequence logos: A new way to display consensus sequences Nucleic Acids Res 1990 18 20 6097-6100 332411 2172928 10.1093/ nar/18.20.6097
    • (1990) Nucleic Acids Res , vol.18 , Issue.20 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 16
    • 33745622868 scopus 로고    scopus 로고
    • Two Sample Logo: A graphical representation of the differences between two sets of sequence alignments
    • 10.1093/bioinformatics/btl151 16632492
    • Vacic V Iakoucheva LM Radivojac P Two Sample Logo: A graphical representation of the differences between two sets of sequence alignments Bioinformatics 2006 22 12 1536-1537 10.1093/bioinformatics/ btl151 16632492
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1536-1537
    • Vacic, V.1    Iakoucheva, L.M.2    Radivojac, P.3
  • 17
    • 33746353437 scopus 로고    scopus 로고
    • Subfamily logos: Visualization of sequence deviations at alignment positions with high information content
    • 1513608 16790056 10.1186/1471-2105-7-313
    • Beitz E Subfamily logos: Visualization of sequence deviations at alignment positions with high information content BMC Bioinformatics 2006 7 313 1513608 16790056 10.1186/1471-2105-7-313
    • (2006) BMC Bioinformatics , vol.7 , pp. 313
    • Beitz, E.1
  • 18
    • 0000071395 scopus 로고
    • Some Distance Properties of Latent Root and Vector Methods Used in Multivariate Analysis
    • Gower JC Some Distance Properties of Latent Root and Vector Methods Used in Multivariate Analysis Biometrika 1966 53 325 &
    • (1966) Biometrika , vol.53 , pp. 325
    • Gower, J.C.1
  • 19
    • 0026547387 scopus 로고
    • Sequence ordinations: A multivariate analysis approach to analysing large sequence data sets
    • 1568121
    • Higgins DG Sequence ordinations: A multivariate analysis approach to analysing large sequence data sets Comput Appl Biosci 1992 8 1 15-22 1568121
    • (1992) Comput Appl Biosci , vol.8 , Issue.1 , pp. 15-22
    • Higgins, D.G.1
  • 20
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • 10.1038/nsb0295-171 7749921
    • Casari G Sander C Valencia A A method to predict functional residues in proteins Nat Struct Biol 1995 2 2 171-178 10.1038/nsb0295-171 7749921
    • (1995) Nat Struct Biol , vol.2 , Issue.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 22
    • 33745599119 scopus 로고    scopus 로고
    • Phylogeny-independent detection of functional residues
    • 10.1093/bioinformatics/btl104 16551661
    • Pazos F Rausell A Valencia A Phylogeny-independent detection of functional residues Bioinformatics 2006 22 12 1440-1448 10.1093/ bioinformatics/btl104 16551661
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1440-1448
    • Pazos, F.1    Rausell, A.2    Valencia, A.3
  • 23
    • 0023557675 scopus 로고
    • Rhythmes saisonniers et composantes stationelles en milieu aquatique I-Description d'un plan d'observations complet par projection de variables
    • Dolédec S Chessel D Rhythmes saisonniers et composantes stationelles en milieu aquatique I-Description d'un plan d'observations complet par projection de variables. Acta Oecologica Oecologica Generalis 1987 8 403-426
    • (1987) Acta Oecologica Oecologica Generalis , vol.8 , pp. 403-426
    • Dolédec, S.1    Chessel, D.2
  • 24
    • 12244289603 scopus 로고    scopus 로고
    • Between-group analysis of microarray data
    • 10.1093/bioinformatics/18.12.1600 12490444
    • Culhane AC Perriere G Considine EC Cotter TG Higgins DG Between-group analysis of microarray data Bioinformatics 2002 18 12 1600-1608 10.1093/ bioinformatics/18.12.1600 12490444
    • (2002) Bioinformatics , vol.18 , Issue.12 , pp. 1600-1608
    • Culhane, A.C.1    Perriere, G.2    Considine, E.C.3    Cotter, T.G.4    Higgins, D.G.5
  • 25
    • 20744439107 scopus 로고    scopus 로고
    • MADE4: An R package for multivariate analysis of gene expression data
    • 10.1093/bioinformatics/bti394 15797915
    • Culhane AC Thioulouse J Perriere G Higgins DG MADE4: An R package for multivariate analysis of gene expression data Bioinformatics 2005 21 11 2789-2790 10.1093/bioinformatics/bti394 15797915
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2789-2790
    • Culhane, A.C.1    Thioulouse, J.2    Perriere, G.3    Higgins, D.G.4
  • 26
    • 3242891674 scopus 로고    scopus 로고
    • SDPpred: A tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins
    • 441529 Web Server issue 15215423 10.1093/nar/gkh391
    • Kalinina OV Novichkov PS Mironov AA Gelfand MS Rakhmaninova AB SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins Nucleic Acids Res 2004 32 Web Server issue W424-8 441529 15215423 10.1093/nar/gkh391
    • (2004) Nucleic Acids Res , vol.32
    • Kalinina, O.V.1    Novichkov, P.S.2    Mironov, A.A.3    Gelfand, M.S.4    Rakhmaninova, A.B.5
  • 28
    • 18144406581 scopus 로고    scopus 로고
    • Solving the protein sequence metric problem
    • 1088356 15851683 10.1073/pnas.0408677102
    • Atchley WR Zhao J Fernandes AD Druke T Solving the protein sequence metric problem Proc Natl Acad Sci U S A 2005 102 18 6395-6400 1088356 15851683 10.1073/pnas.0408677102
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.18 , pp. 6395-6400
    • Atchley, W.R.1    Zhao, J.2    Fernandes, A.D.3    Druke, T.4
  • 30
    • 0001878986 scopus 로고    scopus 로고
    • ADE-4: A multivariate analysis and graphical display software
    • 10.1023/A:1018513530268
    • Thioulouse J Chessel D Dolédec S Olivier JM ADE-4: A multivariate analysis and graphical display software Statistics and Computing 1997 7 1 75-83 10.1023/A:1018513530268
    • (1997) Statistics and Computing , vol.7 , Issue.1 , pp. 75-83
    • Thioulouse, J.1    Chessel, D.2    Dolédec, S.3    Olivier, J.M.4
  • 31
    • 41149089793 scopus 로고    scopus 로고
    • SeqinR 1.0-2: A contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis
    • Springer U. Bastolla, M. Porto, H.E. Roman, Vendruscolo M
    • Charif D Lobry JR SeqinR 1.0-2: A contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis Structural approaches to sequence evolution: Molecules, networks, populations Springer U. Bastolla, M. Porto, H.E. Roman, Vendruscolo M 2006
    • (2006) Structural Approaches to Sequence Evolution: Molecules, Networks, Populations
    • Charif, D.1    Lobry, J.R.2
  • 32
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • 10.1016/0022-2836(94)90032-9 7966282
    • Henikoff S Henikoff JG Position-based sequence weights J Mol Biol 1994 243 4 574-578 10.1016/0022-2836(94)90032-9 7966282
    • (1994) J Mol Biol , vol.243 , Issue.4 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 33
    • 0029977162 scopus 로고    scopus 로고
    • Using substitution probabilities to improve position-specific scoring matrices
    • 8744776
    • Henikoff JG Henikoff S Using substitution probabilities to improve position-specific scoring matrices Comput Appl Biosci 1996 12 2 135-143 8744776
    • (1996) Comput Appl Biosci , vol.12 , Issue.2 , pp. 135-143
    • Henikoff, J.G.1    Henikoff, S.2
  • 35
    • 84886759204 scopus 로고    scopus 로고
    • Pazos et al http://www.pdg.cnb.uam.es/pazos/Xdet_MCdet_Add/
    • Pazos, F.1
  • 36
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • 3447015
    • Saitou N Nei M The neighbor-joining method: A new method for reconstructing phylogenetic trees 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
  • 37
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 308517 7984417 10.1093/nar/22.22.4673
    • Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994 22 22 4673-4680 308517 7984417 10.1093/nar/22.22.4673
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 38
    • 0032568549 scopus 로고    scopus 로고
    • Two amino acid substitutions convert a guanylyl cyclase, RetGC-1, into an adenylyl cyclase
    • 27573 9600905 10.1073/pnas.95.11.5993
    • Tucker CL Hurley JH Miller TR Hurley JB Two amino acid substitutions convert a guanylyl cyclase, RetGC-1, into an adenylyl cyclase Proc Natl Acad Sci U S A 1998 95 11 5993-5997 27573 9600905 10.1073/pnas.95.11.5993
    • (1998) Proc Natl Acad Sci U S A , vol.95 , Issue.11 , pp. 5993-5997
    • Tucker, C.L.1    Hurley, J.H.2    Miller, T.R.3    Hurley, J.B.4
  • 39
    • 0030901637 scopus 로고    scopus 로고
    • Structure of the adenylyl cyclase catalytic core
    • 10.1038/386247a0 9069282
    • Zhang G Liu Y Ruoho AE Hurley JH Structure of the adenylyl cyclase catalytic core Nature 1997 386 6622 247-253 10.1038/386247a0 9069282
    • (1997) Nature , vol.386 , Issue.6622 , pp. 247-253
    • Zhang, G.1    Liu, Y.2    Ruoho, A.E.3    Hurley, J.H.4
  • 40
  • 42
    • 1342288004 scopus 로고    scopus 로고
    • The Jalview Java alignment editor
    • 10.1093/bioinformatics/btg430 14960472
    • Clamp M Cuff J Searle SM Barton GJ The Jalview Java alignment editor Bioinformatics 2004 20 3 426-427 10.1093/bioinformatics/btg430 14960472
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 426-427
    • Clamp, M.1    Cuff, J.2    Searle, S.M.3    Barton, G.J.4


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