-
1
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
-
2
-
-
0034808117
-
Comparing function and structure between entire proteomes
-
Liu J. and Rost B. (2001) Comparing function and structure between entire proteomes. Protein Sci. 10: 1970-1979
-
(2001)
Protein Sci.
, vol.10
, pp. 1970-1979
-
-
Liu, J.1
Rost, B.2
-
3
-
-
0037250635
-
PEP: Predictions for entire proteomes
-
Carter P., Liu J. and Rost B. (2003) PEP: predictions for entire proteomes. Nucleic Acids Res. 31: 410-413
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 410-413
-
-
Carter, P.1
Liu, J.2
Rost, B.3
-
4
-
-
0037252718
-
The Proteome analysis database: A tool for the in silico analysis of whole proteomes
-
Pruess M., Fleischmann W., Kanapin A., Karavidopoulou Y., Kersey P., Kriventseva E. et al. (2003) The Proteome analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31: 414-417
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 414-417
-
-
Pruess, M.1
Fleischmann, W.2
Kanapin, A.3
Karavidopoulou, Y.4
Kersey, P.5
Kriventseva, E.6
-
5
-
-
0347890404
-
-
Reference removed in proof
-
Reference removed in proof
-
-
-
-
6
-
-
0035814904
-
Computational genomics
-
Koonin E. V. (2001) Computational genomics. Curr. Biol. 11: R155-R158
-
(2001)
Curr. Biol.
, vol.11
-
-
Koonin, E.V.1
-
7
-
-
0034734040
-
Automated extraction of information in molecular biology
-
Andrade M. A. and Bork P. (2000) Automated extraction of information in molecular biology. FEBS Lett. 476: 12-17
-
(2000)
FEBS Lett.
, vol.476
, pp. 12-17
-
-
Andrade, M.A.1
Bork, P.2
-
10
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNa interactions at an atomic level
-
Luscombe N. M., Laskowski R. A. and Thornton J. M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29: 2860-2874
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
11
-
-
0035874906
-
From genome to function
-
Thornton J. M. (2001) From genome to function. Science 292: 2095-2097
-
(2001)
Science
, vol.292
, pp. 2095-2097
-
-
Thornton, J.M.1
-
12
-
-
0032919371
-
Protein folds and families: Sequence and structure alignments
-
Holm L. and Sander C. (1999) Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27: 244-247
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 244-247
-
-
Holm, L.1
Sander, C.2
-
13
-
-
0036947904
-
Bioinformatics: Biology by other means
-
Valencia A. (2002) Bioinformatics: biology by other means. Bioinformatics 18: 1551-1552
-
(2002)
Bioinformatics
, vol.18
, pp. 1551-1552
-
-
Valencia, A.1
-
14
-
-
0036601150
-
Computational methods for the prediction of protein interactions
-
Valencia A. and Pazos F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Str. Biol. 12: 368-373
-
(2002)
Curr. Opin. Str. Biol.
, vol.12
, pp. 368-373
-
-
Valencia, A.1
Pazos, F.2
-
15
-
-
0036322695
-
Target space for structural genomics revisited
-
Liu J. and Rost B. (2002) Target space for structural genomics revisited. Bioinformatics 18: 922-933
-
(2002)
Bioinformatics
, vol.18
, pp. 922-933
-
-
Liu, J.1
Rost, B.2
-
19
-
-
0033008596
-
Distribution of protein folds in the three superkingdoms of life
-
Wolf Y., Brenner S., Bash P. and Koonin E. (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res. 9: 17-26
-
(1999)
Genome Res.
, vol.9
, pp. 17-26
-
-
Wolf, Y.1
Brenner, S.2
Bash, P.3
Koonin, E.4
-
20
-
-
0030720480
-
A structural census of the current population of protein sequences
-
Gerstein M. and Levitt M. (1997) A structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. USA 94: 11911-11916
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 11911-11916
-
-
Gerstein, M.1
Levitt, M.2
-
21
-
-
0033034745
-
Automated genome sequence analysis and annotation
-
Andrade M. A., Brown N. P., Leroy C., Hoersch S., de Daruvar A., Reich C. et al. (1999) Automated genome sequence analysis and annotation. Bioinformatics 15: 391-412
-
(1999)
Bioinformatics
, vol.15
, pp. 391-412
-
-
Andrade, M.A.1
Brown, N.P.2
Leroy, C.3
Hoersch, S.4
De Daruvar, A.5
Reich, C.6
-
22
-
-
0027125735
-
What's in a genome?
-
Bork P., Ouzounis C., Sander C., Scharf M., Schneider R. and Sonnhammer E. (1992) What's in a genome? Nature 358: 287
-
(1992)
Nature
, vol.358
, pp. 287
-
-
Bork, P.1
Ouzounis, C.2
Sander, C.3
Scharf, M.4
Schneider, R.5
Sonnhammer, E.6
-
23
-
-
0035117320
-
Genome sequences and great expectations
-
interactions 2000
-
Iliopoulos I., Tsoka S., Andrade M. A., Janssen P., Audit B., Tramontano A. et al. (2001) Genome sequences and great expectations. Genome Biol. 2: interactions 2000
-
(2001)
Genome Biol.
, vol.2
-
-
Iliopoulos, I.1
Tsoka, S.2
Andrade, M.A.3
Janssen, P.4
Audit, B.5
Tramontano, A.6
-
24
-
-
84862343234
-
-
National Library of Medicine (NLM)
-
Airozo D., Allard R., Brylawski B., Canese K., Kenton D., Knecht L. et al. (1999) MEDLINE, vol. 1999. National Library of Medicine (NLM)
-
(1999)
MEDLINE
, vol.1999
-
-
Airozo, D.1
Allard, R.2
Brylawski, B.3
Canese, K.4
Kenton, D.5
Knecht, L.6
-
25
-
-
0346799108
-
Prediction of protein function from protein sequence and structure
-
in press
-
Whisstock J. C. and Lesk A. M. (2003) Prediction of protein function from protein sequence and structure. Quart. Rev. Biophys. in press
-
(2003)
Quart. Rev. Biophys.
-
-
Whisstock, J.C.1
Lesk, A.M.2
-
26
-
-
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. Nat. Struct. Biol. 2: 171-178
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
27
-
-
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
-
28
-
-
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
-
29
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O. and Sowa M. E. (2002) Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Str. Biol. 12: 21-27
-
(2002)
Curr. Opin. Str. Biol.
, vol.12
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
30
-
-
0002218484
-
Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
-
Pupko T., Bell R. E., Mayrose I., Glaser F. and Ben-Tal N. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18: S71-S77
-
(2002)
Bioinformatics
, vol.18
-
-
Pupko, T.1
Bell, R.E.2
Mayrose, I.3
Glaser, F.4
Ben-Tal, N.5
-
31
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F., Pupko T., Paz I., Bell R. E., Bechor-Shental D., Martz E. et al. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
-
32
-
-
0031714858
-
JOY: Protein sequence-structure representation and analysis
-
Mizuguchi K., Deane C. M., Blundell T. L., Johnson M. S. and Overington J. P. (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics 14: 617-623
-
(1998)
Bioinformatics
, vol.14
, pp. 617-623
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Johnson, M.S.4
Overington, J.P.5
-
33
-
-
0036174712
-
Continuum secondary structure captures protein flexibility
-
Andersen C. A. F., Palmer A. G., Brunak S. and Rost B. (2002) Continuum secondary structure captures protein flexibility. Structure 10: 175-184
-
(2002)
Structure
, vol.10
, pp. 175-184
-
-
Andersen, C.A.F.1
Palmer, A.G.2
Brunak, S.3
Rost, B.4
-
34
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann B., Bairoch A., Apweiler R., Blatter M. C., Estreicher A., Gasteiger E. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31: 365-370
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
-
35
-
-
0034737493
-
The role SWISS-PROT and TrEMBL play in the genome research environment
-
Junker V., Contrino S., Fleischmann W., Hermjakob H., Lang F., Magrane M. et al. (2000) The role SWISS-PROT and TrEMBL play in the genome research environment. J. Biotechnol. 78: 221-234
-
(2000)
J. Biotechnol.
, vol.78
, pp. 221-234
-
-
Junker, V.1
Contrino, S.2
Fleischmann, W.3
Hermjakob, H.4
Lang, F.5
Magrane, M.6
-
36
-
-
0035175671
-
The EMBL nucleotide sequence database
-
Stoesser G., Baker W., van Den Broek A., Camon E., Garcia-Pastor M., Kanz C. et al. (2001) The EMBL nucleotide sequence database. Nucleic Acids Res. 29: 17-21
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 17-21
-
-
Stoesser, G.1
Baker, W.2
Van Den Broek, A.3
Camon, E.4
Garcia-Pastor, M.5
Kanz, C.6
-
37
-
-
0033926482
-
Protein sequence databases
-
Apweiler R. (2000) Protein sequence databases. Adv. Protein Chem. 54: 31-71
-
(2000)
Adv. Protein Chem.
, vol.54
, pp. 31-71
-
-
Apweiler, R.1
-
38
-
-
0037174288
-
Bioinformatics methods for the analysis of expression arrays: Data clustering and information extraction
-
Tamames J., Clark D., Herrero J., Dopazo J., Blaschke C., Fernandez J. M. et al. (2002) Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J. Biotechnol. 98: 269-283
-
(2002)
J. Biotechnol.
, vol.98
, pp. 269-283
-
-
Tamames, J.1
Clark, D.2
Herrero, J.3
Dopazo, J.4
Blaschke, C.5
Fernandez, J.M.6
-
39
-
-
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. et al. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Briefing Bioinf. 3: 265-274
-
(2002)
Briefing Bioinf.
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
Gattiker, A.4
Falquet, L.5
Pagni, M.6
-
40
-
-
0036122694
-
Online genomics facilities in the new millennium
-
Frishman D., Kaps A. and Mewes H. W. (2002) Online genomics facilities in the new millennium. Pharmacogenomics 3: 265-271
-
(2002)
Pharmacogenomics
, vol.3
, pp. 265-271
-
-
Frishman, D.1
Kaps, A.2
Mewes, H.W.3
-
42
-
-
0037305939
-
Domains, motifs and clusters in the protein universe
-
Liu J. and Rost B. (2003) Domains, motifs and clusters in the protein universe. Curr. Opin. Chem. Biol. 7: 5-11
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 5-11
-
-
Liu, J.1
Rost, B.2
-
44
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
Rost B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol. 318: 595-608
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 595-608
-
-
Rost, B.1
-
45
-
-
0032950094
-
KIND-a non-redundant protein database
-
Kallberg Y. and Persson B. (1999) KIND-a non-redundant protein database. Bioinformatics 15: 260-261
-
(1999)
Bioinformatics
, vol.15
, pp. 260-261
-
-
Kallberg, Y.1
Persson, B.2
-
46
-
-
0037250525
-
Improvements to CluSTr: The database of SWISS-PROT+TrEMBL protein clusters
-
Kriventseva E. V., Servant F. and Apweiler R. (2003) Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. Nucleic Acids Res. 31: 388-389
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 388-389
-
-
Kriventseva, E.V.1
Servant, F.2
Apweiler, R.3
-
47
-
-
0032776495
-
Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
-
Henikoff S., Henikoff J. G. and Pietrokovski S. (1999) Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 15: 471-479
-
(1999)
Bioinformatics
, vol.15
, pp. 471-479
-
-
Henikoff, S.1
Henikoff, J.G.2
Pietrokovski, S.3
-
48
-
-
0032917195
-
Removing redundancy in SWISS-PROT and TrEMBL
-
O'Donovan C., Martin M. J., Glemet E., Codani J. J. and Apweiler R. (1999) Removing redundancy in SWISS-PROT and TrEMBL. Bioinformatics 15: 258-259
-
(1999)
Bioinformatics
, vol.15
, pp. 258-259
-
-
O'Donovan, C.1
Martin, M.J.2
Glemet, E.3
Codani, J.J.4
Apweiler, R.5
-
49
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li W., Jaroszewski L. and Godzik A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17: 282-283
-
(2001)
Bioinformatics
, vol.17
, pp. 282-283
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
50
-
-
0043122933
-
UniqueProt: Creating representative protein sequence sets
-
Mika S. and Rost B. (2003) UniqueProt: creating representative protein sequence sets. Nucleic Acids Res. 31: 3789-3791
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3789-3791
-
-
Mika, S.1
Rost, B.2
-
51
-
-
0031043927
-
The prion folding problem
-
Harrison P. M., Bamborough P., Daggett V., Prusiner S. and Cohen F. E. (1997) The prion folding problem. Curr. Opin. Str. Biol. 7: 53-59
-
(1997)
Curr. Opin. Str. Biol.
, vol.7
, pp. 53-59
-
-
Harrison, P.M.1
Bamborough, P.2
Daggett, V.3
Prusiner, S.4
Cohen, F.E.5
-
52
-
-
0029828166
-
Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
-
Gaasterland T. and Sensen C. W. (1996) Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie 78: 302-310
-
(1996)
Biochimie
, vol.78
, pp. 302-310
-
-
Gaasterland, T.1
Sensen, C.W.2
-
54
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner M., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P. et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25: 25-29
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Blake, J.A.2
Botstein, D.3
Butler, H.4
Cherry, J.M.5
Davis, A.P.6
-
55
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd A. E., Orengo C. A. and Thornton J. M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
56
-
-
0001619859
-
High-quality protein knowledge resource: SWISS-PROT and TrEMBL
-
O'Donovan C., Martin M. J., Gattiker A., Gasteiger E., Bairoch A. and Apweiler R. (2002) High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Briefing Bioinf. 3: 275-284
-
(2002)
Briefing Bioinf.
, vol.3
, pp. 275-284
-
-
O'Donovan, C.1
Martin, M.J.2
Gattiker, A.3
Gasteiger, E.4
Bairoch, A.5
Apweiler, R.6
-
57
-
-
0345998940
-
Cataloguing proteins in cell cycle control
-
Lieberman, H. (ed), Humana Press, Totowa, NJ
-
Wrzeszczynski K. O. and Rost B. (2003) Cataloguing proteins in cell cycle control. In: Cell Cycle Checkpoint Control Protocols, pp. 219-233, Lieberman, H. (ed), Humana Press, Totowa, NJ
-
(2003)
Cell Cycle Checkpoint Control Protocols
, pp. 219-233
-
-
Wrzeszczynski, K.O.1
Rost, B.2
-
58
-
-
0034308142
-
Practical limits of function prediction
-
Devos D. and Valencia A. (2000) Practical limits of function prediction. Proteins 41: 98-107
-
(2000)
Proteins
, vol.41
, pp. 98-107
-
-
Devos, D.1
Valencia, A.2
-
59
-
-
0036891705
-
Sequence conserved for sub-cellular localization
-
Nair R. and Rost B. (2002) Sequence conserved for sub-cellular localization. Protein Sci. 11: 2836-2847
-
(2002)
Protein Sci.
, vol.11
, pp. 2836-2847
-
-
Nair, R.1
Rost, B.2
-
62
-
-
0034677669
-
Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
-
Wilson C. A., Kreychman J. and Gerstein M. (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297: 233-249
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 233-249
-
-
Wilson, C.A.1
Kreychman, J.2
Gerstein, M.3
-
63
-
-
0347890403
-
-
Reference removed in proof
-
Reference removed in proof
-
-
-
-
65
-
-
0029144085
-
Challenging times for bioinformatics
-
Casari G., Andrade M. A., Bork P., Boyle J., Daruvar A., Ouzounis C. et al. (1995) Challenging times for bioinformatics. Nature 376: 647-648
-
(1995)
Nature
, vol.376
, pp. 647-648
-
-
Casari, G.1
Andrade, M.A.2
Bork, P.3
Boyle, J.4
Daruvar, A.5
Ouzounis, C.6
-
66
-
-
0030219788
-
Computational comparisons of model genomes
-
Ouzounis C., Casari G., Sander C., Tamames J. and Valencia A. (1996) Computational comparisons of model genomes. Trends Biotechnol. 14: 280-285
-
(1996)
Trends Biotechnol.
, vol.14
, pp. 280-285
-
-
Ouzounis, C.1
Casari, G.2
Sander, C.3
Tamames, J.4
Valencia, A.5
-
67
-
-
0033042327
-
Whole-genome sequence annotation: 'Going wrong with confidence'
-
Kyrpides N. C. and Ouzounis C. A. (1999) Whole-genome sequence annotation: 'Going wrong with confidence'. Mol. Microbiol. 32: 886-887
-
(1999)
Mol. Microbiol.
, vol.32
, pp. 886-887
-
-
Kyrpides, N.C.1
Ouzounis, C.A.2
-
68
-
-
18144453832
-
Errors in genome reviews
-
Kyrpides N. C. and Ouzounis C. A. (1998) Errors in genome reviews. Science 281: 1457
-
(1998)
Science
, vol.281
, pp. 1457
-
-
Kyrpides, N.C.1
Ouzounis, C.A.2
-
69
-
-
0034133732
-
Annotations of biochemically uncharacterized open reading frames (ORFs)
-
Mushegian A. R. (2000) Annotations of biochemically uncharacterized open reading frames (ORFs). Mol. Microbiol. 35: 697-698
-
(2000)
Mol. Microbiol.
, vol.35
, pp. 697-698
-
-
Mushegian, A.R.1
-
70
-
-
0035282861
-
Bringing gene order into bacterial shape
-
Tamames J., Gonzalez-Moreno M., Mingorance J., Valencia A. and Vicente M. (2001) Bringing gene order into bacterial shape. Trends Genet. 17: 124-126
-
(2001)
Trends Genet.
, vol.17
, pp. 124-126
-
-
Tamames, J.1
Gonzalez-Moreno, M.2
Mingorance, J.3
Valencia, A.4
Vicente, M.5
-
71
-
-
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
-
72
-
-
0032229196
-
Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
-
Galperin M. Y. and Koonin E. V. (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol. 1: 55-67
-
(1998)
In Silico Biol.
, vol.1
, pp. 55-67
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
73
-
-
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
-
74
-
-
0035753660
-
Quod erat 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. et al. (2001) Quod erat 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
-
75
-
-
0003410183
-
-
Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, Academic Press, New York
-
Webb E. C. (1992) Enzyme Nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, Academic Press, New York
-
(1992)
Enzyme Nomenclature 1992
-
-
Webb, E.C.1
-
76
-
-
0036081347
-
MIPS: A database for genomes and protein sequences
-
Mewes H. W., Frishman D., Guldener U., Mannhaupt G., Mayer K., Mokrejs M. et al. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30: 31-34
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 31-34
-
-
Mewes, H.W.1
Frishman, D.2
Guldener, U.3
Mannhaupt, G.4
Mayer, K.5
Mokrejs, M.6
-
77
-
-
0031887946
-
Wanted: Subcellular localization of proteins based on sequence
-
Eisenhaber F. and Bork P. (1998) Wanted: subcellular localization of proteins based on sequence. Trends Cell Biol. 8: 169-170
-
(1998)
Trends Cell Biol.
, vol.8
, pp. 169-170
-
-
Eisenhaber, F.1
Bork, P.2
-
78
-
-
0034828777
-
Functional versatility and molecular diversity of the metabolic map of Escherichia coli
-
Tsoka S. and Ouzounis C. A. (2001) Functional versatility and molecular diversity of the metabolic map of Escherichia coli. Genome Res. 11: 1503-1510
-
(2001)
Genome Res.
, vol.11
, pp. 1503-1510
-
-
Tsoka, S.1
Ouzounis, C.A.2
-
79
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B. (1999) Twilight zone of protein sequence alignments. Prot. Eng. 12: 85-94
-
(1999)
Prot. Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
80
-
-
0026030641
-
Database of homology-derived structures and the structural meaning of sequence alignment
-
Sander C. and Schneider R. (1991) Database of homology-derived structures and the structural meaning of sequence alignment. Proteins 9: 56-68
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
81
-
-
0029868212
-
Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site
-
Nielsen H., Engelbrecht J., von Heijne G. and Brunak S. (1996) Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site. Proteins 24: 165-177
-
(1996)
Proteins
, vol.24
, pp. 165-177
-
-
Nielsen, H.1
Engelbrecht, J.2
Von Heijne, G.3
Brunak, S.4
-
82
-
-
0030801002
-
Gapped Blast and PSI-Blast: A new generation of protein database search programs
-
Altschul S., Madden T., Shaffer A., Zhang J., Zhang Z., Miller W. et al. (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.1
Madden, T.2
Shaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
83
-
-
0033954256
-
The protein data bank
-
Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H. et al. (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
-
84
-
-
0036467068
-
Alignments grow, secondary structure prediction improves
-
Przybylski D. and Rost B. (2002) Alignments grow, secondary structure prediction improves. Proteins 46: 195-205
-
(2002)
Proteins
, vol.46
, pp. 195-205
-
-
Przybylski, D.1
Rost, B.2
-
85
-
-
0011542799
-
The Pfam protein families database
-
Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S. R. et al. (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
-
87
-
-
0031707505
-
Nucleocytoplasmic transport: The soluble phase
-
Mattaj I. W. and Englmeier L. (1998) Nucleocytoplasmic transport: the soluble phase. Annu. Rev. Biochem. 67: 265-306
-
(1998)
Annu. Rev. Biochem.
, vol.67
, pp. 265-306
-
-
Mattaj, I.W.1
Englmeier, L.2
-
88
-
-
0029979607
-
Common principles of protein translocation across membranes
-
Schatz G. and Dobberstein B. (1996) Common principles of protein translocation across membranes. Science 271: 1519-1526
-
(1996)
Science
, vol.271
, pp. 1519-1526
-
-
Schatz, G.1
Dobberstein, B.2
-
89
-
-
0034664730
-
The debate about transport in the Golgi - Two sides of the same coin?
-
Pelham H. R. and Rothman J. E. (2000) The debate about transport in the Golgi - two sides of the same coin? Cell 102: 713-719
-
(2000)
Cell
, vol.102
, pp. 713-719
-
-
Pelham, H.R.1
Rothman, J.E.2
-
90
-
-
0033909566
-
Protein sorting signals and prediction of subcellular localization
-
Nakai K. (2000) Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem. 54: 277-344
-
(2000)
Adv. Protein Chem.
, vol.54
, pp. 277-344
-
-
Nakai, K.1
-
91
-
-
0033044637
-
Machine learning approaches for the prediction of signal peptides and other protein sorting signals
-
Nielsen H., Brunak S. and von Heijne G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Prot. Eng. 12: 3-9
-
(1999)
Prot. Eng.
, vol.12
, pp. 3-9
-
-
Nielsen, H.1
Brunak, S.2
Von Heijne, G.3
-
93
-
-
0033738137
-
A comparison of signal sequence prediction methods using a test set of signal peptides
-
Menne K. M., Hermjakob H. and Apweiler R. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics 16: 741-742
-
(2000)
Bioinformatics
, vol.16
, pp. 741-742
-
-
Menne, K.M.1
Hermjakob, H.2
Apweiler, R.3
-
94
-
-
0032077533
-
Using neural networks for prediction of the subcellular location of proteins
-
Reinhardt A. and Hubbard T. (1998) Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res. 26: 2230-2235
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 2230-2235
-
-
Reinhardt, A.1
Hubbard, T.2
-
95
-
-
0035367127
-
Whole-genome analysis: Annotations and updates
-
Gaasterland T. and Oprea M. (2001) Whole-genome analysis: annotations and updates. Curr. Opin. Str. Biol. 11: 377-381
-
(2001)
Curr. Opin. Str. Biol.
, vol.11
, pp. 377-381
-
-
Gaasterland, T.1
Oprea, M.2
-
96
-
-
0034331073
-
Finding nuclear localisation signals
-
Cokol M., Nair R. and Rost B. (2000) Finding nuclear localisation signals. EMBO Rep. 1: 411-415
-
(2000)
EMBO Rep.
, vol.1
, pp. 411-415
-
-
Cokol, M.1
Nair, R.2
Rost, B.3
-
97
-
-
0037249644
-
NLSdb: Database of nuclear localization signals
-
Nair R., Carter P. and Rost B. (2003) NLSdb: database of nuclear localization signals. Nucleic Acids Res. 31: 397-399
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 397-399
-
-
Nair, R.1
Carter, P.2
Rost, B.3
-
98
-
-
0020132173
-
Correlation of the amino acid composition of a protein to its structural and biological characteristics
-
Nishikawa K. and Ooi T. (1982) Correlation of the amino acid composition of a protein to its structural and biological characteristics. J. Biochem. 91: 1821-1824
-
(1982)
J. Biochem.
, vol.91
, pp. 1821-1824
-
-
Nishikawa, K.1
Ooi, T.2
-
99
-
-
0026521552
-
The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins
-
Nakashima H. and Nishikawa K. (1992) The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Lett. 303: 141-146
-
(1992)
FEBS Lett.
, vol.303
, pp. 141-146
-
-
Nakashima, H.1
Nishikawa, K.2
-
100
-
-
0025933503
-
Expert system for predicting protein localization sites in gram-negative bacteria
-
Nakai K. and Kanehisa M. (1991) Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11: 95-110
-
(1991)
Proteins
, vol.11
, pp. 95-110
-
-
Nakai, K.1
Kanehisa, M.2
-
101
-
-
0027105007
-
A knowledge base for predicting protein localization sites in eukaryotic cells
-
Nakai K. and Kanehisa M. (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911
-
(1992)
Genomics
, vol.14
, pp. 897-911
-
-
Nakai, K.1
Kanehisa, M.2
-
103
-
-
0029915525
-
Computational method to predict mitochondrially imported proteins and their transit peptides
-
Claros M. G. and Vincens P. (1995) Computational method to predict mitochondrially imported proteins and their transit peptides. Eur. J. Biochem. 241: 779-786
-
(1995)
Eur. J. Biochem.
, vol.241
, pp. 779-786
-
-
Claros, M.G.1
Vincens, P.2
-
104
-
-
0034843744
-
Support vector machine approach for protein subcellular localization prediction
-
Hua S. and Sun Z. (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17: 721-728
-
(2001)
Bioinformatics
, vol.17
, pp. 721-728
-
-
Hua, S.1
Sun, Z.2
-
105
-
-
0031588694
-
Relation between amino acid composition and cellular location of proteins
-
Cedano J., Aloy P., Pérez-Pons J. A. and Querol E. (1997) Relation between amino acid composition and cellular location of proteins. J. Mol. Biol. 266: 594-600
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 594-600
-
-
Cedano, J.1
Aloy, P.2
Pérez-Pons, J.A.3
Querol, E.4
-
106
-
-
0036677029
-
Predicting protein cellular localization using a domain projection method
-
Mott R., Schultz J., Bork P. and Ponting C. P. (2002) Predicting protein cellular localization using a domain projection method. Genome Res. 12: 1168-1174
-
(2002)
Genome Res.
, vol.12
, pp. 1168-1174
-
-
Mott, R.1
Schultz, J.2
Bork, P.3
Ponting, C.P.4
-
108
-
-
0032972509
-
PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization
-
Nakai K. and Horton P. (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24: 34-36
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 34-36
-
-
Nakai, K.1
Horton, P.2
-
109
-
-
0030614959
-
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
-
Nielsen H., Engelbrecht J., Brunak S. and von Heijne G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Prot. Eng. 10: 1-6
-
(1997)
Prot. Eng.
, vol.10
, pp. 1-6
-
-
Nielsen, H.1
Engelbrecht, J.2
Brunak, S.3
Von Heijne, G.4
-
110
-
-
0032935861
-
ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
-
Emanuelsson O., Nielsen H. and von Heijne G. (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8: 978-984
-
(1999)
Protein Sci.
, vol.8
, pp. 978-984
-
-
Emanuelsson, O.1
Nielsen, H.2
Von Heijne, G.3
-
111
-
-
0034714135
-
A Bayesian system integrating expression data with sequence patterns for localizing proteins: Comprehensive application to the yeast genome
-
Drawid A. and Gerstein M. (2000) A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol. 301: 1059-1075
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 1059-1075
-
-
Drawid, A.1
Gerstein, M.2
-
112
-
-
0344118117
-
Better prediction of sub-cellular localization by combining evolutionary and structural information
-
in press
-
Nair R. and Rost B. (2003) Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins, in press
-
(2003)
Proteins
-
-
Nair, R.1
Rost, B.2
-
113
-
-
0037250368
-
The RESID Database of Protein Modifications: 2003 Developments
-
Garavelli J. S. (2003) The RESID Database of Protein Modifications: 2003 developments. Nucleic Acids Res. 31: 499-501
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 499-501
-
-
Garavelli, J.S.1
-
114
-
-
0025945726
-
Improving signal peptide prediction accuracy by simulated neural network
-
Ladunga I., Czakó F., Csabai I. and Geszti T. (1991) Improving signal peptide prediction accuracy by simulated neural network. CABIOS 7: 485-487
-
(1991)
CABIOS
, vol.7
, pp. 485-487
-
-
Ladunga, I.1
Czakó, F.2
Csabai, I.3
Geszti, T.4
-
115
-
-
0032817742
-
How many potentially secreted proteins are contained in a bacterial genome?
-
Schneider G. (1999) How many potentially secreted proteins are contained in a bacterial genome? Gene 237: 113-121
-
(1999)
Gene
, vol.237
, pp. 113-121
-
-
Schneider, G.1
-
116
-
-
0034119780
-
Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites
-
Jagla B. and Schuchhardt J. (2000) Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites. Bioinformatics 16: 245-250
-
(2000)
Bioinformatics
, vol.16
, pp. 245-250
-
-
Jagla, B.1
Schuchhardt, J.2
-
117
-
-
0034697980
-
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
-
Emanuelsson O., Nielsen H., Brunak S. and von Heijne G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300: 1005-1016
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1005-1016
-
-
Emanuelsson, O.1
Nielsen, H.2
Brunak, S.3
Von Heijne, G.4
-
118
-
-
0035782686
-
Prediction of in vivo fates of proteins in the era of genomics and proteomics
-
Nakai K. (2001) Prediction of in vivo fates of proteins in the era of genomics and proteomics. J. Struct. Biol. 134: 103-116
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 103-116
-
-
Nakai, K.1
-
119
-
-
0032539958
-
Peptide design aided by neural networks: Biological activity of artificial signal peptidase I cleavage sites
-
Wrede P., Landt O., Klages S., Fatemi A., Hahn U. and Schneider G. (1998) Peptide design aided by neural networks: biological activity of artificial signal peptidase I cleavage sites. Biochemistry 37: 3588-3593
-
(1998)
Biochemistry
, vol.37
, pp. 3588-3593
-
-
Wrede, P.1
Landt, O.2
Klages, S.3
Fatemi, A.4
Hahn, U.5
Schneider, G.6
-
120
-
-
0036096708
-
Prediction of proteasome cleavage motifs by neural networks
-
Kesimir C., Nussbaum A. K., Schild H., Detours V. and Brunak S. (2002) Prediction of proteasome cleavage motifs by neural networks. Prot. Eng. 15: 287-296
-
(2002)
Prot. Eng.
, vol.15
, pp. 287-296
-
-
Kesimir, C.1
Nussbaum, A.K.2
Schild, H.3
Detours, V.4
Brunak, S.5
-
121
-
-
0037089139
-
Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites
-
Graber J. H., McAllister G. D. and Smith T. F. (2002) Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites. Nucleic Acids Res. 30: 1851-1858
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1851-1858
-
-
Graber, J.H.1
McAllister, G.D.2
Smith, T.F.3
-
122
-
-
0031762518
-
Artificial neural network method for predicting HIV protease cleavage sites in protein
-
Cai Y. D., Yu H. and Chou K. C. (1998) Artificial neural network method for predicting HIV protease cleavage sites in protein. J. Protein Chem. 17: 607-615
-
(1998)
J. Protein Chem.
, vol.17
, pp. 607-615
-
-
Cai, Y.D.1
Yu, H.2
Chou, K.C.3
-
123
-
-
0034813268
-
Sigma a recognition sites in the Bacillus subtilis genome
-
Jarmer H., Larsen T. S., Krogh A., Saxild H. H., Brunak S. and Knudsen S. (2001) Sigma A recognition sites in the Bacillus subtilis genome. Microbiology 147: 2417-2424
-
(2001)
Microbiology
, vol.147
, pp. 2417-2424
-
-
Jarmer, H.1
Larsen, T.S.2
Krogh, A.3
Saxild, H.H.4
Brunak, S.5
Knudsen, S.6
-
124
-
-
0035074032
-
PAProC: A prediction algorithm for proteasomal cleavages available on the www
-
Nussbaum A. K., Kuttler C., Hadeler K. P., Rammensee H. G. and Schild H. (2001) PAProC: a prediction algorithm for proteasomal cleavages available on the www. Immunogenetics 53: 87-94
-
(2001)
Immunogenetics
, vol.53
, pp. 87-94
-
-
Nussbaum, A.K.1
Kuttler, C.2
Hadeler, K.P.3
Rammensee, H.G.4
Schild, H.5
-
125
-
-
0033579464
-
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
-
Blom N., Gammeltoft S. and Brunak S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294: 1351-1362
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 1351-1362
-
-
Blom, N.1
Gammeltoft, S.2
Brunak, S.3
-
126
-
-
0032922002
-
PhosphoBase, a database of phosphorylation sites: Release 2.0
-
Kreegipuu A., Blom N. and Brunak S. (1999) PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res. 27: 237-239
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 237-239
-
-
Kreegipuu, A.1
Blom, N.2
Brunak, S.3
-
127
-
-
0035049164
-
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: Analysis of protein sequence data from complete genomes
-
Eisenhaber B., Bork P. and Eisenhaber F. (2001) Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Prot. Eng. 14: 17-25
-
(2001)
Prot. Eng.
, vol.14
, pp. 17-25
-
-
Eisenhaber, B.1
Bork, P.2
Eisenhaber, F.3
-
128
-
-
0036370537
-
Prediction of glycosylation across the human proteome and the correlation to protein function
-
Gupta R. and Brunak S. (2002) Prediction of glycosylation across the human proteome and the correlation to protein function. Pac. Symp. Biocomput. 310-322
-
(2002)
Pac. Symp. Biocomput.
, pp. 310-322
-
-
Gupta, R.1
Brunak, S.2
-
129
-
-
0031809552
-
NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
-
Hansen J., Lund O., Tolstrup N., Gooley A. A., Williams K. L. and Brunak S. (1998) NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconjugate J. 15: 115-130
-
(1998)
Glycoconjugate J.
, vol.15
, pp. 115-130
-
-
Hansen, J.1
Lund, O.2
Tolstrup, N.3
Gooley, A.A.4
Williams, K.L.5
Brunak, S.6
-
131
-
-
0036290648
-
N-terminal N-myristoylation of proteins: Prediction of substrate proteins from amino acid sequence
-
Maurer-Stroh S., Eisenhaber B. and Eisenhaber F. (2002) N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J. Mol. Biol. 317: 541-557
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 541-557
-
-
Maurer-Stroh, S.1
Eisenhaber, B.2
Eisenhaber, F.3
-
132
-
-
0027133165
-
Function of the gene products in Escherichia coli
-
Riley M. (1993) Function of the gene products in Escherichia coli. Microbiol. Rev. 57: 862-952
-
(1993)
Microbiol. Rev.
, vol.57
, pp. 862-952
-
-
Riley, M.1
-
133
-
-
0036169141
-
Machine learning of functional class from phenotype data
-
Clare A. and King R. D. (2002) Machine learning of functional class from phenotype data. Bioinformatics 18: 160-166
-
(2002)
Bioinformatics
, vol.18
, pp. 160-166
-
-
Clare, A.1
King, R.D.2
-
134
-
-
0034084865
-
Who's your neighbor? New computational approaches for functional genomics
-
Galperin M. Y. and Koonin E. V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18: 609-613
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 609-613
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
135
-
-
0031024670
-
Conserved clusters of functionally related genes in two bacterial genomes
-
Tamames J., Casari G., Ouzounis C. and Valencia A. (1997) Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44
-
(1997)
J. Mol. Evol.
, vol.44
-
-
Tamames, J.1
Casari, G.2
Ouzounis, C.3
Valencia, A.4
-
136
-
-
0033301555
-
Use of contiguity on the chromosome to predict functional coupling
-
Overbeek R., Fonstein M., D'Souza M., Pusch G. D. and Maltsev N. (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1: 93-108
-
(1999)
In Silico Biol.
, vol.1
, pp. 93-108
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
137
-
-
18444390875
-
Prediction of human protein function from post-translational modifications and localization features
-
Jensen L. J., Gupta R., Blom N., Devos D., Tamames J., Kesmir C. et al. (2002) Prediction of human protein function from post-translational modifications and localization features. J. Mol. Biol. 319: 1257-1265
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1257-1265
-
-
Jensen, L.J.1
Gupta, R.2
Blom, N.3
Devos, D.4
Tamames, J.5
Kesmir, C.6
-
138
-
-
0036671947
-
Copper and prion diseases
-
Brown D. R. (2002) Copper and prion diseases. Biochem. Soc. Trans. 30: 742-745
-
(2002)
Biochem. Soc. Trans.
, vol.30
, pp. 742-745
-
-
Brown, D.R.1
-
139
-
-
0036892449
-
Prediction of novel archaeal enzymes from sequence-derived features
-
Jensen L. J., Skovgaard M. and Brunak S. (2002) Prediction of novel archaeal enzymes from sequence-derived features. Protein Sci. 11: 2894-2898
-
(2002)
Protein Sci.
, vol.11
, pp. 2894-2898
-
-
Jensen, L.J.1
Skovgaard, M.2
Brunak, S.3
-
140
-
-
0037460964
-
Prediction of human protein function according to Gene Ontology categories
-
Jensen L. J., Gupta R., Staerfeldt H. H. and Brunak S. (2003) Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19: 635-642
-
(2003)
Bioinformatics
, vol.19
, pp. 635-642
-
-
Jensen, L.J.1
Gupta, R.2
Staerfeldt, H.H.3
Brunak, S.4
-
141
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P., Giot L., Cagney G., Mansfield T. A., Judson R. S., Knight J. R. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
-
142
-
-
0034747028
-
DIP: The database of interacting proteins: 2001 update
-
Xenarios I., Fernandez E., Salwinski L., Duan X. J., Thompson M. J., Marcotte E. M. et al. (2001) DIP: the database of interacting proteins: 2001 update. Nucleic Acids Res. 29: 239-241
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 239-241
-
-
Xenarios, I.1
Fernandez, E.2
Salwinski, L.3
Duan, X.J.4
Thompson, M.J.5
Marcotte, E.M.6
-
143
-
-
0035367880
-
Determination of protein function, evolution and interactions by structural genomics
-
Teichmann S. A., Murzin A. G. and Chothia C. (2001) Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Str. Biol. 11: 354-363
-
(2001)
Curr. Opin. Str. Biol.
, vol.11
, pp. 354-363
-
-
Teichmann, S.A.1
Murzin, A.G.2
Chothia, C.3
-
144
-
-
0036306236
-
On the role of electrostatic interactions in the design of protein-protein interfaces
-
Sheinerman F. B. and Honig B. (2002) On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mol. Biol. 318: 161-177
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 161-177
-
-
Sheinerman, F.B.1
Honig, B.2
-
145
-
-
0034027595
-
Computational genetics: Finding protein function by nonhomology methods
-
Marcotte E. M. (2000) Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Str. Biol. 10: 359-365
-
(2000)
Curr. Opin. Str. Biol.
, vol.10
, pp. 359-365
-
-
Marcotte, E.M.1
-
146
-
-
0034923505
-
Analysis of proteins and proteomes by mass spectrometry
-
Mann M., Hendrickson R. C. and Pandey A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70: 437-473
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 437-473
-
-
Mann, M.1
Hendrickson, R.C.2
Pandey, A.3
-
147
-
-
0036469060
-
Unravelling hot spots in binding interfaces: Progress and challenges
-
DeLano W. (2002) Unravelling hot spots in binding interfaces: progress and challenges. Curr. Opin. Str. Biol. 12: 14-20
-
(2002)
Curr. Opin. Str. Biol.
, vol.12
, pp. 14-20
-
-
DeLano, W.1
-
148
-
-
0035424708
-
Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments
-
Michnick S. W. (2001) Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments. Curr. Opin. Str. Biol. 11: 472-477
-
(2001)
Curr. Opin. Str. Biol.
, vol.11
, pp. 472-477
-
-
Michnick, S.W.1
-
149
-
-
0037250152
-
STRING: A database of predicted functional associations between proteins
-
von Mering C., Huynen M., Jaeggi D., Schmidt S., Bork P. and Snel B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31: 258-261
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 258-261
-
-
Von Mering, C.1
Huynen, M.2
Jaeggi, D.3
Schmidt, S.4
Bork, P.5
Snel, B.6
-
150
-
-
0037250151
-
InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes
-
Ng S. K., Zhang Z., Tan S. H. and Lin K. (2003) InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res. 31: 251-254
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 251-254
-
-
Ng, S.K.1
Zhang, Z.2
Tan, S.H.3
Lin, K.4
-
151
-
-
0037249217
-
Whole-proteome interaction mining
-
Bock J. R. and Gough D. A. (2003) Whole-proteome interaction mining. Bioinformatics 19: 125-134
-
(2003)
Bioinformatics
, vol.19
, pp. 125-134
-
-
Bock, J.R.1
Gough, D.A.2
-
152
-
-
0037245913
-
BIND: The biomolecular interaction network database
-
Bader G. D., Betel D. and Hogue C. W. (2003) BIND: the biomolecular interaction network database. Nucleic Acids Res. 31: 248-250
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
153
-
-
0037250158
-
InterPreTS: Protein interaction prediction through tertiary structure
-
Aloy P. and Russell R. B. (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19: 161-162
-
(2003)
Bioinformatics
, vol.19
, pp. 161-162
-
-
Aloy, P.1
Russell, R.B.2
-
154
-
-
0037059461
-
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
-
Tong A. H., Drees B., Nardelli G., Bader G. D., Brannetti B., Castagnoli L. et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321-324
-
(2002)
Science
, vol.295
, pp. 321-324
-
-
Tong, A.H.1
Drees, B.2
Nardelli, G.3
Bader, G.D.4
Brannetti, B.5
Castagnoli, L.6
-
155
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith G. R. and Sternberg M. J. (2002) Prediction of protein-protein interactions by docking methods. Curr. Opin. Str. Biol. 12: 28-35
-
(2002)
Curr. Opin. Str. Biol.
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.2
-
156
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin A. C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
-
157
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho Y., Gruhler A., Heilbut A., Bader G. D., Moore L., Adams S. L. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.L.6
-
158
-
-
11244311539
-
Of truth and pathways: Chasing bits of information through myriads of articles
-
Krauthammer M., Kra P., Iossifov I., Gomez S. M., Hripcsak G., Hatzivassiloglou V. et al. (2002) Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics 18: S249-S257
-
(2002)
Bioinformatics
, vol.18
-
-
Krauthammer, M.1
Kra, P.2
Iossifov, I.3
Gomez, S.M.4
Hripcsak, G.5
Hatzivassiloglou, V.6
-
160
-
-
0035002541
-
Mining literature for protein-protein interactions
-
Marcotte E. M., Xenarios I. and Eisenberg D. (2001) Mining literature for protein-protein interactions. Bioinformatics 17: 359-363
-
(2001)
Bioinformatics
, vol.17
, pp. 359-363
-
-
Marcotte, E.M.1
Xenarios, I.2
Eisenberg, D.3
-
161
-
-
0035967862
-
Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction
-
Gromiha M. M. and Selvaraj S. (2001) Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J. Mol. Biol. 310: 27-32
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 27-32
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
162
-
-
0036088133
-
DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions
-
Xenarios I., Salwinski L., Duan X. J., Higney P., Kim S. M. and Eisenberg D. (2002) DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-305
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
Salwinski, L.2
Duan, X.J.3
Higney, P.4
Kim, S.M.5
Eisenberg, D.6
-
164
-
-
0034766349
-
Mining functional information associated with expression arrays
-
Blaschke C., Oliveros J. C. and Valencia A. (2001) Mining functional information associated with expression arrays. Funct. Integr. Genomics 1: 256-268
-
(2001)
Funct. Integr. Genomics
, vol.1
, pp. 256-268
-
-
Blaschke, C.1
Oliveros, J.C.2
Valencia, A.3
-
165
-
-
0035236048
-
GENIES : A natural-language processing system for the extraction of molecular pathways from journal articles
-
Friedman C., Kra P., Yu H., Krauthammer M. and Rzhetsky A. (2001) GENIES : a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17: S74-S82
-
(2001)
Bioinformatics
, vol.17
-
-
Friedman, C.1
Kra, P.2
Yu, H.3
Krauthammer, M.4
Rzhetsky, A.5
-
166
-
-
0033832615
-
Predicting protein function by genomic context
-
Huynen M., Snel B., Lathe W. and Bork P. (2000) Predicting protein function by genomic context. Genome Res. 4: 1204-1210
-
(2000)
Genome Res.
, vol.4
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe, W.3
Bork, P.4
-
167
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar T., Snel B., Huynen M. and Bork P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324-328
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
168
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte E. M., Pellegrini M., Ng H. L., Rice D. W., Yeates T. O. and Eisenberg D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
169
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright A. J., Ilipoulos I., Kyrpides N. C. and Ouzounis C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Ilipoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
170
-
-
0031610846
-
Constructing multigenome views of whole microbial genomes
-
Gaasterland T. and Ragan M. A. (1998) Constructing multigenome views of whole microbial genomes. Microb. Comp. Genomics 3: 177-192
-
(1998)
Microb. Comp. Genomics
, vol.3
, pp. 177-192
-
-
Gaasterland, T.1
Ragan, M.A.2
-
171
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F. and Valencia A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Prot. Eng. 14: 609-614
-
(2001)
Prot. Eng.
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
172
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
Goh C. S., Bogan A. A., Joachimiak M., Walther D. and Cohen F. E. (2000) Co-evolution of proteins with their interaction partners. J. Mol. Biol. 299: 283-293
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 283-293
-
-
Goh, C.S.1
Bogan, A.A.2
Joachimiak, M.3
Walther, D.4
Cohen, F.E.5
-
173
-
-
0036435908
-
Co-evolutionary analysis reveals insights into protein-protein interactions
-
Goh C. S. and Cohen F. E. (2002) Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324: 177-192
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 177-192
-
-
Goh, C.S.1
Cohen, F.E.2
-
174
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos F., Helmer-Citterich M., Ausiello G. and Valencia A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 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
-
175
-
-
0036568319
-
In silico two-hybrid system for the selection of physically interacting protein pairs
-
Pazos F. and Valencia A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219-227
-
(2002)
Proteins
, vol.47
, pp. 219-227
-
-
Pazos, F.1
Valencia, A.2
-
176
-
-
0035943340
-
Correlated sequence-signatures as markers of protein-protein interaction
-
Sprinzak E. and Margalit H. (2001) Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol. 311: 681-692
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 681-692
-
-
Sprinzak, E.1
Margalit, H.2
-
177
-
-
0035672003
-
Probabilistic prediction of unknown metabolic and signal-transduction networks
-
Gomez S. M., Lo S. H. and Rzhetsky A. (2001) Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics 159: 1291-1298
-
(2001)
Genetics
, vol.159
, pp. 1291-1298
-
-
Gomez, S.M.1
Lo, S.H.2
Rzhetsky, A.3
-
178
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P. and Russell R. B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA 99: 5896-5901
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
179
-
-
0037110589
-
MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
-
Lu L., Lu H. and Skolnick J. (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364
-
(2002)
Proteins
, vol.49
, pp. 350-364
-
-
Lu, L.1
Lu, H.2
Skolnick, J.3
-
180
-
-
0344480548
-
Inferring sub-cellular localisation through automated lexical analysis
-
Nair, R. and Rost B. (2002) Inferring sub-cellular localisation through automated lexical analysis. Bioinformatics 18: S78-S86
-
(2002)
Bioinformatics
, vol.18
-
-
Nair, R.1
Rost, B.2
|