-
1
-
-
0033150686
-
From protein structure to function
-
Orengo,C.A.,Todd,A.E. and Thornton,J.M. (1999) From protein structure to function. Curr. Opin. Struct. Biol., 9, 374-382.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 374-382
-
-
Orengo, C.A.1
Todd, A.E.2
Thornton, J.M.3
-
2
-
-
0012671418
-
Defining the mandate of proteomics in the post-genomics era: Workshop report
-
Kenyon,G.L., DeMarini,D.M., Fuchs,E., Galas,D.J., Kirsch,J.F., Leyh,T.S., Moos,W.H., Petsko,G.A., Ringe,D., Rubin,G.M. et al. (2002) Defining the mandate of proteomics in the post-genomics era: workshop report. Mol. Cell. Proteomics, 1, 763-780.
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 763-780
-
-
Kenyon, G.L.1
DeMarini, D.M.2
Fuchs, E.3
Galas, D.J.4
Kirsch, J.F.5
Leyh, T.S.6
Moos, W.H.7
Petsko, G.A.8
Ringe, D.9
Rubin, G.M.10
-
3
-
-
0346731042
-
Automatic prediction of protein function
-
Rost,B., Liu,J., Nair,R., Wrzeszczynski,K.O. and Ofran,Y. (2003) Automatic prediction of protein function. Cell. Mol. Life Sci. 60, 2637-2650.
-
(2003)
Cell Mol. Life Sci.
, vol.60
, pp. 2637-2650
-
-
Rost, B.1
Liu, J.2
Nair, R.3
Wrzeszczynski, K.O.4
Ofran, Y.5
-
4
-
-
0035865078
-
Human disease genes
-
Jimenez-Sanchez,G., Childs,B. and Valle,D. (2001) Human disease genes. Nature, 409, 853-855.
-
(2001)
Nature
, vol.409
, pp. 853-855
-
-
Jimenez-Sanchez, G.1
Childs, B.2
Valle, D.3
-
5
-
-
0033990061
-
Flexible sequence similarity searching with the FASTA3 program package
-
Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.
-
(2000)
Methods Mol. Biol.
, vol.132
, pp. 185-219
-
-
Pearson, W.R.1
-
6
-
-
0029889221
-
Local alignment statistics
-
Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Meth. Enzymol., 266, 460-480.
-
(1996)
Meth. Enzymol.
, vol.266
, pp. 460-480
-
-
Altschul, S.F.1
Gish, W.2
-
7
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
8
-
-
0031743421
-
Profile hidden Markov models
-
Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
9
-
-
0035424599
-
Intrinsic errors in genome annotation
-
Devos,D. and Valencia,A. (2001) Intrinsic errors in genome annotation. Trends Genet., 17, 429-431.
-
(2001)
Trends Genet.
, vol.17
, pp. 429-431
-
-
Devos, D.1
Valencia, A.2
-
10
-
-
0142106373
-
How well is enzyme function conserved as a function of pairwise sequence identity?
-
Tian,W. and Skolnick,J. (2003) How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol. 333, 863-882.
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 863-882
-
-
Tian, W.1
Skolnick, J.2
-
11
-
-
0001290045
-
PROSITE: A documented database using patterns and profiles as motif descriptors
-
Sigrist,C.J., Cerutti,L., Hulo,N., Gattiker,A., Falquet,L., Pagni,M., Bairoch,A. and Bucher,P. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinformatics, 3, 265-274.
-
(2002)
Brief Bioinformatics
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
Gattiker, A.4
Falquet, L.5
Pagni, M.6
Bairoch, A.7
Bucher, P.8
-
12
-
-
0033957801
-
PRINTS-S: The database formerly known as PRINTS
-
Attwood,T.K., Croning,M.D., Flower,D.R., Lewis,A.P., Mabey,J.E., Scordis,P., Selley,J.N. and Wright,W. (2000) PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Res., 28, 225-227.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 225-227
-
-
Attwood, T.K.1
Croning, M.D.2
Flower, D.R.3
Lewis, A.P.4
Mabey, J.E.5
Scordis, P.6
Selley, J.N.7
Wright, W.8
-
13
-
-
0033977579
-
Increased coverage of protein families with the blocks database servers
-
Henikoff,J.G., Greene,E.A., Pietrokovski,S. and Henikoff,S. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 28, 228-230.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 228-230
-
-
Henikoff, J.G.1
Greene, E.A.2
Pietrokovski, S.3
Henikoff, S.4
-
14
-
-
2942549126
-
A structural study for the optimisation of functional motifs encoded in protein sequences
-
Via,A. and Helmer-Citterich,M. (2004) A structural study for the optimisation of functional motifs encoded in protein sequences. BMC Bioinformatics, 5, 50.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 50
-
-
Via, A.1
Helmer-Citterich, M.2
-
15
-
-
0029587166
-
A method to predict functional residues in proteins
-
Casari,G., Sander,C. and Valencia,A. (1995) A method to predict functional residues in proteins. Nature Struct. Biol., 2 171-178.
-
(1995)
Nature Struct. Biol.
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
16
-
-
0037470597
-
Automatic methods for predicting functionally important residues
-
del Sol Mesa,A., Pazos,F. and Valencia,A. (2003) Automatic methods for predicting functionally important residues. J. Mol. Biol. 326, 1289-1302.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1289-1302
-
-
del Sol Mesa, A.1
Pazos, F.2
Valencia, A.3
-
17
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge,O., Bourne,H.R. and Cohen,F.E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
18
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon,A., Graur,D. and Ben-Tal,N. (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol., 307, 447-463.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
19
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf,R., Xenarios,I. and Eisenberg,D. (2001) Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol., 307, 1487-1502.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
20
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli,S.S. and Russell,R.B. (2000) Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol., 303, 61-76.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
21
-
-
0011542799
-
The Pfam protein families database
-
Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
22
-
-
0037397439
-
Definitions of enzyme function for the structural genomics era
-
Babbitt,P.C. (2003) Definitions of enzyme function for the structural genomics era. Curr. Opin. Chem. Biol., 7, 230-237.
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 230-237
-
-
Babbitt, P.C.1
-
23
-
-
0033963089
-
The ENZYME database in 2000
-
Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 304-305
-
-
Bairoch, A.1
-
24
-
-
0033957834
-
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
-
Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
25
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa,M. and Goto,S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
26
-
-
0034923923
-
Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
-
Gerlt,J.A. and Babbitt,P.C. (2001) Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem., 70, 209-246.
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 209-246
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
27
-
-
0036683309
-
Plasticity of enzyme active sites
-
Todd,A.E, Orengo, C.A. and Thornton,J.M. (2002) Plasticity of enzyme active sites. Trends Biochem. Sci., 27, 419-426.
-
(2002)
Trends Biochem. Sci.
, vol.27
, pp. 419-426
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
28
-
-
0031897589
-
Predicting functions from protein sequences - Where are the bottlenecks?
-
Bork,P. and Koonin,E.V. (1998) Predicting functions from protein sequences - where are the bottlenecks? Nature Genet., 18 313-318.
-
(1998)
Nature Genet.
, vol.18
, pp. 313-318
-
-
Bork, P.1
Koonin, E.V.2
-
29
-
-
0035753660
-
Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences
-
RESEARCH0051
-
Iyer,L.M., Aravind,L., Bork,P., Hofmann,K., Mushegian,A.R., Zhulin,I.B. and Koonin,E.V. (2001) Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol., 2, RESEARCH0051.
-
(2001)
Genome Biol.
, vol.2
-
-
Iyer, L.M.1
Aravind, L.2
Bork, P.3
Hofmann, K.4
Mushegian, A.R.5
Zhulin, I.B.6
Koonin, E.V.7
-
31
-
-
0023984847
-
Optimal alignments in linear space
-
Myers,E.W. and Miller,W. (1988) Optimal alignments in linear space. Comput. Appl. Biosci., 4, 11-17.
-
(1988)
Comput. Appl. Biosci.
, vol.4
, pp. 11-17
-
-
Myers, E.W.1
Miller, W.2
-
32
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
33
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
34
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
-
(1975)
Biochim. Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
35
-
-
0033954256
-
The Protein Data Bank
-
Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 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
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
36
-
-
0029670395
-
glc locus of Escherichia coli: Characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein
-
Pellicer,M.T., Badia,J., Aguilar,J. and Baldoma,L. (1996) glc locus of Escherichia coli: characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein. J. Bacteriol., 178, 2051-2059.
-
(1996)
J. Bacteriol.
, vol.178
, pp. 2051-2059
-
-
Pellicer, M.T.1
Badia, J.2
Aguilar, J.3
Baldoma, L.4
-
37
-
-
0015523117
-
Glycolate oxidoreductase in Escherichia coli
-
Lord,J.M. (1972) Glycolate oxidoreductase in Escherichia coli. Biochim. Biophys. Acta, 267, 227-237.
-
(1972)
Biochim. Biophys. Acta
, vol.267
, pp. 227-237
-
-
Lord, J.M.1
-
38
-
-
0036136174
-
Utilization of L-ascorbate by Escherichia coli K-12: Assignments of functions to products of the yjf-sga and yia-sgb operons
-
Yew,W.S. and Gerlt,J.A. (2002) Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. J. Bacteriol., 184, 302-306.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 302-306
-
-
Yew, W.S.1
Gerlt, J.A.2
-
39
-
-
3042842012
-
YbdK is a carboxylate-amine ligase with a gamma-glutamyl:cysteine ligase activity: Crystal structure and enzymatic assays
-
Lehmann,C., Doseeva,V., Pullalarevu,S., Krajewski,W., Howard,A. and Herzberg,O. (2004) YbdK is a carboxylate-amine ligase with a gamma-glutamyl:cysteine ligase activity: crystal structure and enzymatic assays. Proteins, 56, 376-383.
-
(2004)
Proteins
, vol.56
, pp. 376-383
-
-
Lehmann, C.1
Doseeva, V.2
Pullalarevu, S.3
Krajewski, W.4
Howard, A.5
Herzberg, O.6
-
40
-
-
2542594077
-
Identifying latent enzyme activities: Substrate ambiguity within modern bacterial sugar kinases
-
Miller,B.G. and Raines,R.T. (2004) Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases. Biochemistry, 43, 6387-6392.
-
(2004)
Biochemistry
, vol.43
, pp. 6387-6392
-
-
Miller, B.G.1
Raines, R.T.2
-
41
-
-
0035095613
-
Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli
-
Donnenberg,M.S. and Whittam,T.S. (2001) Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli. J. Clin. Invest., 107, 539-548.
-
(2001)
J. Clin. Invest.
, vol.107
, pp. 539-548
-
-
Donnenberg, M.S.1
Whittam, T.S.2
-
42
-
-
0345531106
-
Enzyme-specific profiles for genome annotation: PRIAM
-
Claudel-Renard,C., Chevalet,C., Faraut,T. and Kahn,D. (2003) Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res., 31, 6633-6639.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6633-6639
-
-
Claudel-Renard, C.1
Chevalet, C.2
Faraut, T.3
Kahn, D.4
-
43
-
-
0033119399
-
Errors in genome annotation
-
Brenner,S.E. (1999) Errors in genome annotation. Trends Genet., 15, 132-133.
-
(1999)
Trends Genet.
, vol.15
, pp. 132-133
-
-
Brenner, S.E.1
-
44
-
-
0036175276
-
The past, present and future of genome-wide re-annotation
-
COMMENT2001
-
Ouzounis, C.A. and Karp,P.D. (2002) The past, present and future of genome-wide re-annotation. Genome Biol., 3, COMMENT2001.
-
(2002)
Genome Biol.
, vol.3
-
-
Ouzounis, C.A.1
Karp, P.D.2
|