-
1
-
-
0031576355
-
Do aligned sequences share the same fold?
-
Abagyan,R.A. and Batalov,S. (1997) Do aligned sequences share the same fold? J. Mol. Biol., 273, 355-368.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 355-368
-
-
Abagyan, R.A.1
Batalov, S.2
-
2
-
-
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
-
3
-
-
0003063899
-
-
Submitted for publication
-
Arvestad,L., Ivansson,L., Lagergren,J. and Elofsson,A. (2000) What is the best method to determine if two proteins are related? A study on the structural and evolutionary significance of pairwise protein sequence alignments. Submitted for publication.
-
(2000)
What Is the Best Method to Determine if Two Proteins Are Related? A Study on the Structural and Evolutionary Significance of Pairwise Protein Sequence Alignments
-
-
Arvestad, L.1
Ivansson, L.2
Lagergren, J.3
Elofsson, A.4
-
4
-
-
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
-
5
-
-
0033976458
-
The Pfam protein families database
-
Bateman,A., Birney,E., Durbin,R., Eddy,S.R., Howe,K.L. and Sonnhammer,E.L. (2000) The Pfam protein families database. Nucleic Acids Res., 28, 263-266.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 263-266
-
-
Bateman, A.1
Birney, E.2
Durbin, R.3
Eddy, S.R.4
Howe, K.L.5
Sonnhammer, E.L.6
-
6
-
-
0034777598
-
Clustering protein sequences-structure prediction by transitive homology
-
Bolten,E., Schliep,A., Schneckener,S., Schomburg,D. and Schrader,R. (2001) Clustering protein sequences-structure prediction by transitive homology. Bioinformatics, 10, 935-942.
-
(2001)
Bioinformatics
, vol.10
, pp. 935-942
-
-
Bolten, E.1
Schliep, A.2
Schneckener, S.3
Schomburg, D.4
Schrader, R.5
-
7
-
-
0032568596
-
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
-
Brenner,S.E., Chothia,C. and Hubbard,T.J. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 6073-6078
-
-
Brenner, S.E.1
Chothia, C.2
Hubbard, T.J.3
-
8
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
-
(1986)
EMBO J.
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
9
-
-
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
-
10
-
-
0033944826
-
Generage: A robust algorithm for sequence clustering and domain detection
-
Enright,A.J. and Ouzounis,C.A. (2000) Generage: a robust algorithm for sequence clustering and domain detection. Bioinformatics, 16, 451-457.
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
11
-
-
0031762837
-
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
-
Gerstein,M. (1998) Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics, 14, 707-714.
-
(1998)
Bioinformatics
, vol.14
, pp. 707-714
-
-
Gerstein, M.1
-
12
-
-
0032940544
-
Scop: A structural classification of proteins database
-
Hubbard,T.J.P., Ailey,B., Brenner,S.E., Murzin,A.G. and Chothia,C. (1999) Scop: a structural classification of proteins database. Nucleic Acids Res., 27, 254-256.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 254-256
-
-
Hubbard, T.J.P.1
Ailey, B.2
Brenner, S.E.3
Murzin, A.G.4
Chothia, C.5
-
14
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
15
-
-
0031876711
-
A set-theoretic approach to database searching and clustering
-
Krause,A. and Vingron,M. (1998) A set-theoretic approach to database searching and clustering. Bioinformatics, 14, 430-438.
-
(1998)
Bioinformatics
, vol.14
, pp. 430-438
-
-
Krause, A.1
Vingron, M.2
-
16
-
-
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
-
17
-
-
0033940118
-
Rsdb: Representative protein sequence databases have high information content
-
Park,J., Holm,L., Heger,A. and Chothia,C. (2000) Rsdb: representative protein sequence databases have high information content. Bioinformatics, 16, 458-464.
-
(2000)
Bioinformatics
, vol.16
, pp. 458-464
-
-
Park, J.1
Holm, L.2
Heger, A.3
Chothia, C.4
-
18
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park,J., Teichmann,S.A., Hubbard,T. and Chothia,C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 349-354
-
-
Park, J.1
Teichmann, S.A.2
Hubbard, T.3
Chothia, C.4
-
19
-
-
0029006770
-
Comparison of methods for searching protein sequence databases
-
Pearson,W.R. (1995) Comparison of methods for searching protein sequence databases. Protein Sci., 4, 1145-1160.
-
(1995)
Protein Sci.
, vol.4
, pp. 1145-1160
-
-
Pearson, W.R.1
-
20
-
-
0030776390
-
Identifying distantly related protein sequences
-
Pearson,W.R. (1997) Identifying distantly related protein sequences. Comput. Appl. Biosci., 13, 325-332.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 325-332
-
-
Pearson, W.R.1
-
21
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
-
(1999)
Protein Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
22
-
-
0032940341
-
Combining sensitive database searches with multiple intermediates to detect distant homologues
-
in process citation
-
Salamov,A.A., Suwa,M., Orengo,C.A. and Swindells,M.B. (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues [in process citation]). Protein Eng., 12, 95-100.
-
(1999)
Protein Eng.
, vol.12
, pp. 95-100
-
-
Salamov, A.A.1
Suwa, M.2
Orengo, C.A.3
Swindells, M.B.4
-
23
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander,C. and Schneider,R. (1991) Database of homology-derived protein 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
-
25
-
-
0004112038
-
-
C. Addison Wesley, Reading, MA
-
Sedgewick,R. (1990) Algorithms in C. Addison Wesley, Reading, MA.
-
(1990)
Algorithms
-
-
Sedgewick, R.1
-
26
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
27
-
-
0035022822
-
Limits of homology detection by pairwise sequence comparison
-
Spang,R. and Vingron,M. (2001) Limits of homology detection by pairwise sequence comparison. Bioinformatics, 17, 338-342.
-
(2001)
Bioinformatics
, vol.17
, pp. 338-342
-
-
Spang, R.1
Vingron, M.2
-
29
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
30
-
-
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, 4673-1680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-11680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
31
-
-
0028234758
-
Rapid and accurate estimates of statistical significance for sequence data base searches
-
Waterman,M.S. and Vingron,M. (1994) Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl Acad. Sci. USA, 91, 4625-1628.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 4625-11628
-
-
Waterman, M.S.1
Vingron, M.2
-
32
-
-
0001514262
-
Statistics of local complexity in amino acid sequences and sequence databases
-
Wootton,J.C. and Federhen,S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem., 17, 149-163. Software available at http://blast.wustl.edu/ pub/seg
-
(1993)
Comput. Chem.
, vol.17
, pp. 149-163
-
-
Wootton, J.C.1
Federhen, S.2
-
33
-
-
0032726692
-
Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space
-
Yona,G., Linial,N. and Linial,M. (1999) Protomap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins, 37, 360-378.
-
(1999)
Proteins
, vol.37
, pp. 360-378
-
-
Yona, G.1
Linial, N.2
Linial, M.3
|