-
1
-
-
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
-
2
-
-
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
-
3
-
-
0035167572
-
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
-
Dietmann,S., Park,J., Notredame,C., Heger,A., Lappe,M. and Holm,L. (2001) A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res., 29, 55-57.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 55-57
-
-
Dietmann, S.1
Park, J.2
Notredame, C.3
Heger, A.4
Lappe, M.5
Holm, L.6
-
4
-
-
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
-
5
-
-
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
-
6
-
-
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
-
7
-
-
0029918694
-
The FSSP database: Fold classification based on structure-structure alignment of proteins
-
Holm,L. and Sander,C. (1996) The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res., 24, 206-209.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 206-209
-
-
Holm, L.1
Sander, C.2
-
8
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
9
-
-
0035970287
-
Consistency analysis of similarity between multiple alignments: Prediction of protein function and fold structure from analysis of local sequence motifs
-
Kunin,V., Chan,B., Sitbon,E., Lithwick,G. and Pietrokovski,S. (2001) Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. J. Mol. Biol., 307, 939-949.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 939-949
-
-
Kunin, V.1
Chan, B.2
Sitbon, E.3
Lithwick, G.4
Pietrokovski, S.5
-
10
-
-
0036086410
-
Recent improvements to the SMART domain-based sequence annotation resource
-
Letunic,I., Goodstadt,L., Dickens,N.J., Doerks,T., Schultz,J., Mott,R., Ciccarelli,F., Copley,R.R., Ponting,C.P. and Bork,P. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 30, 242-244.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 242-244
-
-
Letunic, I.1
Goodstadt, L.2
Dickens, N.J.3
Doerks, T.4
Schultz, J.5
Mott, R.6
Ciccarelli, F.7
Copley, R.R.8
Ponting, C.P.9
Bork, P.10
-
11
-
-
0041886960
-
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
-
Mittelman,D., Sadreyev,R. and Grishin,N. (2003) Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics, 19, 1531-1539.
-
(2003)
Bioinformatics
, vol.19
, pp. 1531-1539
-
-
Mittelman, D.1
Sadreyev, R.2
Grishin, N.3
-
12
-
-
0037440190
-
Finding weak similarities between proteins by sequence profile comparison
-
Panchenko,A.R. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res., 31, 683-689.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 683-689
-
-
Panchenko, A.R.1
-
13
-
-
0029789461
-
Searching databases of conserved sequence regions by aligning protein multiple-alignments
-
Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 3836-3845
-
-
Pietrokovski, S.1
-
14
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
-
(2000)
Protein Sci.
, vol.9
, pp. 232-241
-
-
Rychlewski, L.1
Jaroszewski, L.2
Li, W.3
Godzik, A.4
-
15
-
-
0141634362
-
Profile-profile comparisons by COMPASS predict intricate homologies between protein families
-
Sadreyev,R.I., Baker,D. and Grishin,N.V. (2003) Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci., 2262-2272.
-
(2003)
Protein Sci.
, pp. 2262-2272
-
-
Sadreyev, R.I.1
Baker, D.2
Grishin, N.V.3
-
16
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev,R.I. and Grishin,N.V. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 317-336
-
-
Sadreyev, R.I.1
Grishin, N.V.2
-
17
-
-
0034237578
-
Large-scale comparison of protein sequence alignment algorithms with structure alignments
-
Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6-22.
-
(2000)
Proteins
, vol.40
, pp. 6-22
-
-
Sauder, J.M.1
Arthur, J.W.2
Dunbrack Jr., R.L.3
-
18
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
19
-
-
0038438514
-
IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
-
Schaffer,A.A., Wolf,Y.I., Ponting,C.P., Koonin,E.V., Aravind,L. and Altschul,S.F. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 15, 1000-1011.
-
(1999)
Bioinformatics
, vol.15
, pp. 1000-1011
-
-
Schaffer, A.A.1
Wolf, Y.I.2
Ponting, C.P.3
Koonin, E.V.4
Aravind, L.5
Altschul, S.F.6
-
20
-
-
0032568655
-
SMART, a simple modular architecture research tool: Identification of signaling domains
-
Schultz,J., Milpetz,F., Bork,P. and Ponting,C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
21
-
-
0033028454
-
PSIC: Profile extraction from sequence alignments with position-specific counts of independent observations
-
Sunyaev,S.R., Eisenhaber,F., Rodchenkov,I.V., Eisenhaber,B., Tumanyan,V.G. and Kuznetsov,E.N. (1999) PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng., 12, 387-394.
-
(1999)
Protein Eng.
, vol.12
, pp. 387-394
-
-
Sunyaev, S.R.1
Eisenhaber, F.2
Rodchenkov, I.V.3
Eisenhaber, B.4
Tumanyan, V.G.5
Kuznetsov, E.N.6
-
22
-
-
0036307493
-
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
-
Yona,G. and Levitt,M. (2002) Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 1257-1275
-
-
Yona, G.1
Levitt, M.2
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