-
1
-
-
0035838976
-
Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
-
Aloy P., Querol E., Aviles F., Sternberg M. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311:2001;395-408.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.3
Sternberg, M.4
-
2
-
-
0034990892
-
Sequence- and structure-based protein function prediction from genomic information
-
Baxter S.M., Fetrow J.S. Sequence- and structure-based protein function prediction from genomic information. Curr. Opin. Drug Discov. Dev. 4:2001;291-295.
-
(2001)
Curr. Opin. Drug Discov. Dev.
, vol.4
, pp. 291-295
-
-
Baxter, S.M.1
Fetrow, J.S.2
-
3
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C., Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:1986;823-826.
-
(1986)
EMBO J.
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
4
-
-
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., Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297:2000;233-249.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 233-249
-
-
Wilson, C.A.1
Kreychman, J.2
Gerstein, M.3
-
5
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318:2002;595-608.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 595-608
-
-
Rost, B.1
-
7
-
-
0032776495
-
Blocks + a non-redundant database of protein alignment blocks derived from multiple compilations
-
Henikoff S., Henikoff J.G., Pietrokovski S. Blocks + a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics. 15:1999;471-479.
-
(1999)
Bioinformatics
, vol.15
, pp. 471-479
-
-
Henikoff, S.1
Henikoff, J.G.2
Pietrokovski, S.3
-
8
-
-
18444381153
-
PRINTS and PRINTS-S shed light on protein ancestry
-
Attwood T.K., Blythe M.J., Flower D.R., Gaulton A., Mabey J.E., Maudling N., et al. PRINTS and PRINTS-S shed light on protein ancestry. Nucl. Acids Res. 30:2002;239-241.
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 239-241
-
-
Attwood, T.K.1
Blythe, M.J.2
Flower, D.R.3
Gaulton, A.4
Mabey, J.E.5
Maudling, N.6
-
9
-
-
0011542799
-
The Pfam protein families database
-
Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., et al. The Pfam protein families database. Nucl. Acids Res. 30:2002;276-280.
-
(2002)
Nucl. 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
-
10
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
11
-
-
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., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
-
(1997)
Nucl. 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
-
12
-
-
0031866670
-
ACHEdb: The database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server
-
Cousin X., Hotelier T., Giles K., Toutant J.P., Chatonnet A. aCHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server. Nucl. Acids Res. 26:1998;226-228.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 226-228
-
-
Cousin, X.1
Hotelier, T.2
Giles, K.3
Toutant, J.P.4
Chatonnet, A.5
-
13
-
-
0032944238
-
The PROSITE database, its status in 1999
-
Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucl. Acids Res. 27:1999;215-219.
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 215-219
-
-
Hofmann, K.1
Bucher, P.2
Falquet, L.3
Bairoch, A.4
-
15
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf R., Xenarios I., Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 307:2001;1487-1502.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
16
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O., Bourne H.R., Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:1996;342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
17
-
-
0036300444
-
Structural clusters of evolutionary trace residues are statistically significant and common in proteins
-
Madabushi S., Yao H., Marsh M., Kristensen D.M., Philippi A., Sowa M.E., Lichtarge O. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J. Mol. Biol. 316:2002;139-154.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 139-154
-
-
Madabushi, S.1
Yao, H.2
Marsh, M.3
Kristensen, D.M.4
Philippi, A.5
Sowa, M.E.6
Lichtarge, O.7
-
18
-
-
0037423759
-
An accurate, sensitive, and scalable method to identify functional sites in protein structures
-
Yao H., Kristensen D.M., Mihalek I., Sowa M.E., Shaw C., Kimmel M., et al. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol. 326:2003;255-261.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 255-261
-
-
Yao, H.1
Kristensen, D.M.2
Mihalek, I.3
Sowa, M.E.4
Shaw, C.5
Kimmel, M.6
-
19
-
-
0043130640
-
Automated construction of structural motifs for predicting functional sites on protein structures
-
Liang M.P., Brutlag D.L., Altman R.B. Automated construction of structural motifs for predicting functional sites on protein structures. Pac. Symp. Biocomput. 2003;204-215.
-
(2003)
Pac. Symp. Biocomput.
, pp. 204-215
-
-
Liang, M.P.1
Brutlag, D.L.2
Altman, R.B.3
-
20
-
-
0036406643
-
A new method to detect related function among proteins independent of sequence and fold homology
-
Schmitt S., Kuhn D., Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 323:2002;387-406.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
21
-
-
0032483312
-
Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
-
Fetrow J.S., Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281:1998;949-968.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 949-968
-
-
Fetrow, J.S.1
Skolnick, J.2
-
22
-
-
0032843737
-
Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily
-
Fetrow J.S., Siew N., Skolnick J. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. FASEB J. 13:1999;1866-1874.
-
(1999)
FASEB J.
, vol.13
, pp. 1866-1874
-
-
Fetrow, J.S.1
Siew, N.2
Skolnick, J.3
-
23
-
-
0032475938
-
Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity
-
Fetrow J.S., Godzik A., Skolnick J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 282:1998;703-711.
-
(1998)
J. Mol. Biol.
, vol.282
, pp. 703-711
-
-
Fetrow, J.S.1
Godzik, A.2
Skolnick, J.3
-
24
-
-
0033194958
-
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), Enzyme Supplement 5 (1999)
-
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), Enzyme Supplement 5 (1999). Eur. J. Biochem. 264:1999;610-650.
-
(1999)
Eur. J. Biochem.
, vol.264
, pp. 610-650
-
-
-
25
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissing H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissing, H.6
-
26
-
-
0030610593
-
Crystal structure of Kex1deltap, a prohormone-processing carboxypeptidase from Saccharomyces cerevisiae
-
Shilton B.H., Thomas D.Y., Cygler M. Crystal structure of Kex1deltap, a prohormone-processing carboxypeptidase from Saccharomyces cerevisiae. Biochemistry. 36:1997;9002-9012.
-
(1997)
Biochemistry
, vol.36
, pp. 9002-9012
-
-
Shilton, B.H.1
Thomas, D.Y.2
Cygler, M.3
-
27
-
-
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., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
28
-
-
0026540411
-
The alpha/beta hydrolase fold
-
Ollis D.L., Cheah E., Cygler M., Dijkstra B., Frolow F., Franken S.M., et al. The alpha/beta hydrolase fold. Protein Eng. 5:1992;197-211.
-
(1992)
Protein Eng.
, vol.5
, pp. 197-211
-
-
Ollis, D.L.1
Cheah, E.2
Cygler, M.3
Dijkstra, B.4
Frolow, F.5
Franken, S.M.6
-
29
-
-
0035782660
-
Enhanced functional annotation of protein sequences via the use of structural descriptors
-
Di Gennaro J.A., Siew N., Hoffman B.T., Zhang L., Skolnick J., Neilson L.I., Fetrow J.S. Enhanced functional annotation of protein sequences via the use of structural descriptors. J. Struct. Biol. 134:2001;232-245.
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 232-245
-
-
Di Gennaro, J.A.1
Siew, N.2
Hoffman, B.T.3
Zhang, L.4
Skolnick, J.5
Neilson, L.I.6
Fetrow, J.S.7
-
31
-
-
0032568596
-
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
-
Brenner S.E., Chothia C., Hubbard T.J. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA. 95:1998;6073-6078.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 6073-6078
-
-
Brenner, S.E.1
Chothia, C.2
Hubbard, T.J.3
-
32
-
-
0035162594
-
RefSeq and LocusLink: NCBI gene-centered resources
-
Pruitt K.D., Maglott D.R. RefSeq and LocusLink: NCBI gene-centered resources. Nucl. Acids Res. 29:2001;137-140.
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
33
-
-
0029759927
-
Structural basis for inhibition of receptor protein-tyrosine phosphatase-alpha by dimerization
-
Bilwes A.M., den Hertog J., Hunter T., Noel J.P. Structural basis for inhibition of receptor protein-tyrosine phosphatase-alpha by dimerization. Nature. 382:1996;555-559.
-
(1996)
Nature
, vol.382
, pp. 555-559
-
-
Bilwes, A.M.1
Den Hertog, J.2
Hunter, T.3
Noel, J.P.4
-
34
-
-
0037032835
-
The protein kinase complement of the human genome
-
Manning G., Whyte D.B., Martinez R., Hunter T., Sudarsanam S. The protein kinase complement of the human genome. Science. 298:2002;1912-1934.
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
35
-
-
0029020282
-
Protein kinases 6. The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification
-
Hanks S.K., Hunter T. Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J. 9:1995;576-596.
-
(1995)
FASEB J.
, vol.9
, pp. 576-596
-
-
Hanks, S.K.1
Hunter, T.2
-
36
-
-
0026604926
-
Regulation of fatty acid and cholesterol metabolism by the AMP-activated protein kinase
-
Hardie D.G. Regulation of fatty acid and cholesterol metabolism by the AMP-activated protein kinase. Biochim. Biophys. Acta. 1123:1992;231-238.
-
(1992)
Biochim. Biophys. Acta
, vol.1123
, pp. 231-238
-
-
Hardie, D.G.1
-
37
-
-
0034710302
-
Protein kinases and phosphatases in the Drosophila genome
-
Morrison D.K., Murakami M.S., Cleghon V. Protein kinases and phosphatases in the Drosophila genome. J. Cell Biol. 150:2000;F57-F62.
-
(2000)
J. Cell Biol.
, vol.150
-
-
Morrison, D.K.1
Murakami, M.S.2
Cleghon, V.3
-
38
-
-
0031773843
-
Rice has two distinct classes of protein kinase genes related to SNF1 of Saccharomyces cerevisiae, which are differently regulated in early seed development
-
Takano M., Kajiya-Kanegae H., Funatsuki H., Kikuchi S. Rice has two distinct classes of protein kinase genes related to SNF1 of Saccharomyces cerevisiae, which are differently regulated in early seed development. Mol. Gen. Genet. 260:1998;388-394.
-
(1998)
Mol. Gen. Genet.
, vol.260
, pp. 388-394
-
-
Takano, M.1
Kajiya-Kanegae, H.2
Funatsuki, H.3
Kikuchi, S.4
-
39
-
-
0035951457
-
A new family of IKK-related kinases may function as I kappa B kinase kinases
-
Peters R.T., Maniatis T. A new family of IKK-related kinases may function as I kappa B kinase kinases. Biochim. Biophys. Acta. 2:2001;M57-M62.
-
(2001)
Biochim. Biophys. Acta
, vol.2
-
-
Peters, R.T.1
Maniatis, T.2
-
40
-
-
0037069193
-
Inaugural article: Finding important sites in protein sequences
-
Bickel P.J., Kechris K.J., Spector P.C., Wedemayer G.J., Glazer A.N. Inaugural article: finding important sites in protein sequences. Proc. Natl Acad. Sci. USA. 99:2002;14764-14771.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 14764-14771
-
-
Bickel, P.J.1
Kechris, K.J.2
Spector, P.C.3
Wedemayer, G.J.4
Glazer, A.N.5
-
41
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli S.S., Russell R.B. Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol. 303:2000;61-76.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
42
-
-
0034090247
-
A method to predict residues conferring functional differences between related proteins: Application to MAP kinase pathways
-
Caffrey D.R., O'Neill L.A., Shields D.C. A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways. Protein Sci. 9:2000;655-670.
-
(2000)
Protein Sci.
, vol.9
, pp. 655-670
-
-
Caffrey, D.R.1
O'neill, L.A.2
Shields, D.C.3
-
43
-
-
0037342222
-
A path from primary protein sequence to ligand recognition
-
Kho R., Baker B.L., Newman J.V., Jack R.M., Sem D.S., Villar H.O., Hansen M.R. A path from primary protein sequence to ligand recognition. Proteins: Struct. Funct. Genet. 50:2003;589-599.
-
(2003)
Proteins: Struct. Funct. Genet.
, vol.50
, pp. 589-599
-
-
Kho, R.1
Baker, B.L.2
Newman, J.V.3
Jack, R.M.4
Sem, D.S.5
Villar, H.O.6
Hansen, M.R.7
-
44
-
-
0036568353
-
Classification of proteins based on the properties of the ligand- binding site: The case of adenine-binding proteins
-
Cappello V., Tramontano A., Koch U. Classification of proteins based on the properties of the ligand- binding site: the case of adenine-binding proteins. Proteins: Struct. Funct. Genet. 47:2002;106-115.
-
(2002)
Proteins: Struct. Funct. Genet.
, vol.47
, pp. 106-115
-
-
Cappello, V.1
Tramontano, A.2
Koch, U.3
-
45
-
-
0036145469
-
Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function
-
Friedberg I., Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. Protein Sci. 11:2002;350-360.
-
(2002)
Protein Sci.
, vol.11
, pp. 350-360
-
-
Friedberg, I.1
Margalit, H.2
-
46
-
-
0034635976
-
Predicting ligand-binding function in families of bacterial receptors
-
Johnson J.M., Church G.M. Predicting ligand-binding function in families of bacterial receptors. Proc. Natl Acad. Sci. USA. 97:2000;3965-3970.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 3965-3970
-
-
Johnson, J.M.1
Church, G.M.2
-
47
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O., Sowa M.E. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12:2002;21-27.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.E.2
-
48
-
-
0034785827
-
Structural and evolutionary relationships among protein tyrosine phosphatase domains
-
Andersen J.N., Mortensen O.H., Peters G.H., Drake P.G., Iversen L.F., Olsen O.H., et al. Structural and evolutionary relationships among protein tyrosine phosphatase domains. Mol. Cell Biol. 21:2001;7117-7136.
-
(2001)
Mol. Cell Biol.
, vol.21
, pp. 7117-7136
-
-
Andersen, J.N.1
Mortensen, O.H.2
Peters, G.H.3
Drake, P.G.4
Iversen, L.F.5
Olsen, O.H.6
-
49
-
-
0034788453
-
Tyrosine kinase inhibitors: From rational design to clinical trials
-
Traxler P., Bold G., Buchdunger E., Caravatti G., Furet P., Manley P., et al. Tyrosine kinase inhibitors: from rational design to clinical trials. Med. Res. Rev. 21:2001;499-512.
-
(2001)
Med. Res. Rev.
, vol.21
, pp. 499-512
-
-
Traxler, P.1
Bold, G.2
Buchdunger, E.3
Caravatti, G.4
Furet, P.5
Manley, P.6
-
50
-
-
0036019064
-
The use of computational methods in the discovery and design of kinase inhibitors
-
Woolfrey J.R., Weston G.S. The use of computational methods in the discovery and design of kinase inhibitors. Curr. Pharm. Des. 8:2002;1527-1545.
-
(2002)
Curr. Pharm. Des.
, vol.8
, pp. 1527-1545
-
-
Woolfrey, J.R.1
Weston, G.S.2
-
51
-
-
0035866002
-
Defrosting the frozen approximation: PROSPECTOR - A new approach to threading
-
Skolnick J., Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins: Struct. Funct. Genet. 42:2001;319-331.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.42
, pp. 319-331
-
-
Skolnick, J.1
Kihara, D.2
-
52
-
-
0026747032
-
PATMAT: A searching and extraction program for sequence, pattern and block queries and databases
-
Wallace J.C., Henikoff S. PATMAT: a searching and extraction program for sequence, pattern and block queries and databases. Comput. Appl. Biosci. 8:1992;249-254.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 249-254
-
-
Wallace, J.C.1
Henikoff, S.2
-
53
-
-
0033388381
-
FingerPRINTScan: Intelligent searching of the PRINTS motif database
-
Scordis P., Flower D.R., Attwood T.K. FingerPRINTScan: intelligent searching of the PRINTS motif database. Bioinformatics. 15:1999;799-806.
-
(1999)
Bioinformatics
, vol.15
, pp. 799-806
-
-
Scordis, P.1
Flower, D.R.2
Attwood, T.K.3
-
54
-
-
0031743421
-
Profile hidden Markov models
-
Eddy S.R. Profile hidden Markov models. Bioinformatics. 14:1998;755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
|