-
1
-
-
0029889221
-
Local alignment statistics
-
ALTSCHUL, S.F., and GISH, W. (1996). Local alignment statistics. Methods Enzymol 266, 460-480.
-
(1996)
Methods Enzymol
, vol.266
, pp. 460-480
-
-
Altschul, S.F.1
Gish, W.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., 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.F.1
Madden, T.L.2
Schaffer, A.A.3
-
3
-
-
0033957801
-
PRINTS-S: The database formerly known as PRINTS
-
ATTWOOD, T.K., CRONING, M.D., FLOWER, D.R., et al. (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
-
4
-
-
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
-
5
-
-
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
-
6
-
-
10044221079
-
A new statistical approach to predicting aromatic hydroxylation sites. Comparison with model-based approaches
-
BORODINA, Y., RUDIK, A., FILIMONOV, D., et al. (2004). A new statistical approach to predicting aromatic hydroxylation sites. Comparison with model-based approaches. J Chem Inf Comput Sci 44, 1998-2009.
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 1998-2009
-
-
Borodina, Y.1
Rudik, A.2
Filimonov, D.3
-
7
-
-
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
-
8
-
-
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
-
9
-
-
0034308142
-
Practical limits of functional prediction
-
DEVOS, D., and VALENCIA, A. (2000). Practical limits of functional prediction. Proteins 41, 98-107.
-
(2000)
Proteins
, vol.41
, pp. 98-107
-
-
Devos, D.1
Valencia, A.2
-
10
-
-
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
-
11
-
-
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
-
12
-
-
0000992784
-
Chemical Similarity Assessment through multilevel neighborhoods of atoms: Definition and comparison with the other descriptors
-
FILIMONOV, D., POROIKOV, V., BORODINA, Y., et al. (1999). Chemical Similarity Assessment through multilevel neighborhoods of atoms: definition and comparison with the other descriptors. J Chem Inf Comput Sci 39, 666-670.
-
(1999)
J Chem Inf Comput Sci
, vol.39
, pp. 666-670
-
-
Filimonov, D.1
Poroikov, V.2
Borodina, Y.3
-
13
-
-
0642279119
-
Use of structural MNA descriptors for designing profiles of protein families
-
FOMENKO, A.E., SOBOLEV, B.N., FILIMONOV, D.A., et al. (2003). Use of structural MNA descriptors for designing profiles of protein families. Biofizika 48, 595-605.
-
(2003)
Biofizika
, vol.48
, pp. 595-605
-
-
Fomenko, A.E.1
Sobolev, B.N.2
Filimonov, D.A.3
-
14
-
-
0031666414
-
Analogous enzymes: Independent inventions in enzyme evolution
-
GALPERIN, M.Y., WALKER, D.R., and KOONIN, E.V. (1998). Analogous enzymes: independent inventions in enzyme evolution. Genome Res 8, 779-790.
-
(1998)
Genome Res
, vol.8
, pp. 779-790
-
-
Galperin, M.Y.1
Walker, D.R.2
Koonin, E.V.3
-
15
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignment
-
HANNENHALLI, S.S., and RUSSEL, R.B. (2000). Analysis and prediction of functional sub-types from protein sequence alignment. J Mol Biol 303, 61-76.
-
(2000)
J Mol Biol
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russel, R.B.2
-
16
-
-
0033977579
-
Increased coverage of protein families with the blocks database servers
-
HENIKOFF, J.G., GREENE, E.A., PIETROKOVSKI, S., et al. (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
-
17
-
-
0029785147
-
Mapping the protein universe
-
HOLM, L., and SANDER, C. (1996). Mapping the protein universe. Science 273, 595-602.
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
18
-
-
1642452921
-
Automated selections of positions determining-functional specificity of proteins by comparative analysis of orthologous groups in protein families
-
KALININA, O.V., MIRONOV, A.A., GELFAND, M.S., et al. (2004). Automated selections of positions determining-functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci 13, 443-456.
-
(2004)
Protein Sci
, vol.13
, pp. 443-456
-
-
Kalinina, O.V.1
Mironov, A.A.2
Gelfand, M.S.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
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
LIGHTARGE, 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
-
-
Lightarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
21
-
-
0027764344
-
Protein sequence alignment: A strategy for the hierarchical analysis of residue conservation
-
LIVINGSTONE, C.D., and BARTON, G.J. (1993). Protein sequence alignment: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 9, 745-756.
-
(1993)
Comput Appl Biosci
, vol.9
, pp. 745-756
-
-
Livingstone, C.D.1
Barton, G.J.2
-
22
-
-
0036352010
-
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
-
MIRNY, L.A., and GELFAND, M.S. (2002). Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 321, 7-20.
-
(2002)
J Mol Biol
, vol.321
, pp. 7-20
-
-
Mirny, L.A.1
Gelfand, M.S.2
-
23
-
-
0030777303
-
CATH-a hierarchic classification of protein domain structures
-
ORENGO, C.A., MICHIE, A.D., JONES, S., et al. (1997). CATH-a hierarchic classification of protein domain structures. Structure 15, 1093-1108.
-
(1997)
Structure
, vol.15
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
-
24
-
-
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
-
25
-
-
84964803288
-
PASS: Prediction of biological activity spectra for substances
-
C. Helma, eds. Marcel Dekker, New York
-
POROIKOV, V., and FILIMONOV, D. (2005). PASS: prediction of biological activity spectra for substances. In Predictive Toxicology. C. Helma, eds. (Marcel Dekker, New York, pp. 459-478.
-
(2005)
Predictive Toxicology
, pp. 459-478
-
-
Poroikov, V.1
Filimonov, D.2
-
26
-
-
0037205399
-
Substrate recognition drives the evolution of serine proteases
-
ROSE, T., and DI CERA, E. (2002). Substrate recognition drives the evolution of serine proteases. J Biol Chem 277, 19243-19246.
-
(2002)
J Biol Chem
, vol.277
, pp. 19243-19246
-
-
Rose, T.1
Di Cera, E.2
-
27
-
-
0346731042
-
Automatic prediction of protein function
-
ROST, B., LIU, J., and NAIR, R., et al. (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
-
28
-
-
0001290045
-
PROSITE: A documented database using patterns and profiles as motif descriptors
-
SIGRIST, C.J., CERUTTI, L., HULO, N., et al. (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3, 265-274.
-
(2002)
Brief Bioinform
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
-
29
-
-
0032698873
-
Protein folds, functions and evolution
-
THORNTON, J.M., ORENGO, C.A., TODD, A.E., et al. (1999). Protein folds, functions and evolution. J Mol Biol 293, 333-342.
-
(1999)
J Mol Biol
, vol.293
, pp. 333-342
-
-
Thornton, J.M.1
Orengo, C.A.2
Todd, A.E.3
-
30
-
-
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
-
31
-
-
13444280436
-
EFICAz: A comprehensive approach for accurate genome-scale enzyme function inference
-
TIAN, W., ARAKAKI, A.K., and SKOLNICK, J. (2004). EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res 32, 6226-6239.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6226-6239
-
-
Tian, W.1
Arakaki, A.K.2
Skolnick, J.3
-
32
-
-
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
-
34
-
-
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
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