-
1
-
-
81255138862
-
Enzyme function initiative
-
Gerlt, J. A., Allen, K. N., Almo, S. C., Armstrong, R. N., Babbitt, P. C., Cronan, J. E., Dunaway-Mariano, D., Imker, H. J., Jacobson, M. P., Minor, W. et al. (2011) Enzyme Function Initiative. Biochemistry, 50, 9950-9962.
-
(2011)
Biochemistry
, vol.50
, pp. 9950-9962
-
-
Gerlt, J.A.1
Allen, K.N.2
Almo, S.C.3
Armstrong, R.N.4
Babbitt, P.C.5
Cronan, J.E.6
Dunaway-Mariano, D.7
Imker, H.J.8
Jacobson, M.P.9
Minor, W.10
-
2
-
-
84883152491
-
The COMBREX project: Design, methodology, and initial results
-
Anton, B. P., Chang, Y. C., Brown, P., Choi, H. P., Faller, L. L., Guleria, J., Hu, Z., Klitgord, N., Levy-Moonshine, A., Maksad, A. et al. (2013) The COMBREX project: design, methodology, and initial results. PLoS Biol., 11, e1001638.
-
(2013)
PLoS Biol.
, vol.11
, pp. e1001638
-
-
Anton, B.P.1
Chang, Y.C.2
Brown, P.3
Choi, H.P.4
Faller, L.L.5
Guleria, J.6
Hu, Z.7
Klitgord, N.8
Levy-Moonshine, A.9
Maksad, A.10
-
3
-
-
84874663959
-
A large-scale evaluation of computational protein function prediction
-
Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A. et al. (2013) A large-scale evaluation of computational protein function prediction. Nat. Methods, 10, 221-227.
-
(2013)
Nat. Methods
, vol.10
, pp. 221-227
-
-
Radivojac, P.1
Clark, W.T.2
Oron, T.R.3
Schnoes, A.M.4
Wittkop, T.5
Sokolov, A.6
Graim, K.7
Funk, C.8
Verspoor, K.9
Ben-Hur, A.10
-
4
-
-
84876586862
-
HAMAP in 2013, new developments in the protein family classification and annotation system
-
Pedruzzi, I., Rivoire, C., Auchincloss, A. H., Coudert, E., Keller, G., De Castro, E., Baratin, D., Cuche, B. A., Bougueleret, L., Poux, S. et al. (2013) HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res., 41, D584-D589.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D584-D589
-
-
Pedruzzi, I.1
Rivoire, C.2
Auchincloss, A.H.3
Coudert, E.4
Keller, G.5
De Castro, E.6
Baratin, D.7
Cuche, B.A.8
Bougueleret, L.9
Poux, S.10
-
5
-
-
84874253819
-
Gene Ontology annotations and resources
-
Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Li, N., Sitnikov, D., Bridges, S., Burgess, S., Buza, T., McCarthy, F. et al. (2013) Gene Ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D530-D535
-
-
Blake, J.A.1
Dolan, M.2
Drabkin, H.3
Hill, D.P.4
Li, N.5
Sitnikov, D.6
Bridges, S.7
Burgess, S.8
Buza, T.9
McCarthy, F.10
-
6
-
-
74549221383
-
Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
-
Schnoes, A. M., Brown, S. D., Dodevski, I. and Babbitt, P. C. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605.
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000605
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
7
-
-
84885451642
-
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB
-
Bell, M. J., Collison, M. and Lord, P. (2013) Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PLoS One, 8, e75541.
-
(2013)
PLoS One
, vol.8
, pp. e75541
-
-
Bell, M.J.1
Collison, M.2
Lord, P.3
-
8
-
-
12244283680
-
Modeling the percolation of annotation errors in a database of protein sequences
-
Gilks, W. R., Audit, B., De Angelis, D., Tsoka, S. and Ouzounis, C. A. (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics, 18, 1641-1649.
-
(2002)
Bioinformatics
, vol.18
, pp. 1641-1649
-
-
Gilks, W.R.1
Audit, B.2
De Angelis, D.3
Tsoka, S.4
Ouzounis, C.A.5
-
9
-
-
84946069451
-
UniProt: A hub for protein information
-
UniProt Consortium. (2014) UniProt: a hub for protein information. Nucleic Acids Res., doi:10.1093/nar/gku989.
-
(2014)
Nucleic Acids Res.
-
-
UniProt Consortium1
-
10
-
-
84891822189
-
Ensembl Genomes 2013: Scaling up access to genome-wide data
-
Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S., Humphrey, J., Kerhornou, A., Khobova, J. et al. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res., 42, D546-D552.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D546-D552
-
-
Kersey, P.J.1
Allen, J.E.2
Christensen, M.3
Davis, P.4
Falin, L.J.5
Grabmueller, C.6
Hughes, D.S.7
Humphrey, J.8
Kerhornou, A.9
Khobova, J.10
-
11
-
-
84887343997
-
Genome sequence of Xanthomonas fuscans subsp. Fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads
-
Darrasse, A., Carrere, S., Barbe, V., Boureau, T., Arrieta-Ortiz, M. L., Bonneau, S., Briand, M., Brin, C., Cociancich, S., Durand, K. et al. (2013) Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics, 14, 761.
-
(2013)
BMC Genomics
, vol.14
, pp. 761
-
-
Darrasse, A.1
Carrere, S.2
Barbe, V.3
Boureau, T.4
Arrieta-Ortiz, M.L.5
Bonneau, S.6
Briand, M.7
Brin, C.8
Cociancich, S.9
Durand, K.10
-
12
-
-
84892496453
-
Genome degeneration and adaptation in a nascent stage of symbiosis
-
Oakeson, K. F., Gil, R., Clayton, A. L., Dunn, D. M., Von Niederhausern, A. C., Hamil, C., Aoyagi, A., Duval, B., Baca, A., Silva, F. J. et al. (2014) Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol. Evol., 6, 76-93.
-
(2014)
Genome Biol. Evol.
, vol.6
, pp. 76-93
-
-
Oakeson, K.F.1
Gil, R.2
Clayton, A.L.3
Dunn, D.M.4
Von Niederhausern, A.C.5
Hamil, C.6
Aoyagi, A.7
Duval, B.8
Baca, A.9
Silva, F.J.10
-
13
-
-
0042423439
-
Automated annotation of microbial proteomes in SWISS-PROT
-
Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J., Lachaize, C. et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem., 27, 49-58.
-
(2003)
Comput. Biol. Chem.
, vol.27
, pp. 49-58
-
-
Gattiker, A.1
Michoud, K.2
Rivoire, C.3
Auchincloss, A.H.4
Coudert, E.5
Lima, T.6
Kersey, P.7
Pagni, M.8
Sigrist, C.J.9
Lachaize, C.10
-
14
-
-
0030093114
-
A flexible motif search technique based on generalized profiles
-
Bucher, P., Karplus, K., Moeri, N. and Hofmann, K. (1996) A flexible motif search technique based on generalized profiles. Comput. Chem., 20, 3-23.
-
(1996)
Comput. Chem.
, vol.20
, pp. 3-23
-
-
Bucher, P.1
Karplus, K.2
Moeri, N.3
Hofmann, K.4
-
15
-
-
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., Bairoch, A. and Bucher, P. (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
Gattiker, A.4
Falquet, L.5
Pagni, M.6
Bairoch, A.7
Bucher, P.8
-
16
-
-
0028158905
-
Improving the sensitivity of the sequence profile method
-
Luthy, R., Xenarios, I. and Bucher, P. (1994) Improving the sensitivity of the sequence profile method. Protein Sci., 3, 139-146.
-
(1994)
Protein Sci.
, vol.3
, pp. 139-146
-
-
Luthy, R.1
Xenarios, I.2
Bucher, P.3
-
17
-
-
0000228203
-
-
Dayhoff, M. O., Schwartz, R. and Orcutt, B. C. (1978), Atlas of protein sequence and structure, Vol. 5, pp. 345-358.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, pp. 345-358
-
-
Dayhoff, M.O.1
Schwartz, R.2
Orcutt, B.C.3
-
18
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. and Henikoff, J. G. (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A, 89, 10915-10919.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
33745203038
-
The biochemistry of sirtuins
-
Sauve, A. A., Wolberger, C., Schramm, V. L. and Boeke, J. D. (2006) The biochemistry of sirtuins. Annu. Rev. Biochem., 75, 435-465.
-
(2006)
Annu. Rev. Biochem.
, vol.75
, pp. 435-465
-
-
Sauve, A.A.1
Wolberger, C.2
Schramm, V.L.3
Boeke, J.D.4
-
20
-
-
2942564591
-
Sirtuins: Sir2-related NAD-dependent protein deacetylases
-
North, B. J. and Verdin, E. (2004) Sirtuins: Sir2-related NAD-dependent protein deacetylases. Genome Biol., 5, 224.
-
(2004)
Genome Biol.
, vol.5
, pp. 224
-
-
North, B.J.1
Verdin, E.2
-
21
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh, K. and Standley, D. M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol., 30, 772-780.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
22
-
-
65449188232
-
Jalview version 2-A multiple sequence alignment editor and analysis workbench
-
Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. and Barton, G. J. (2009) Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.3
Clamp, M.4
Barton, G.J.5
-
23
-
-
79954529507
-
ProtTest 3: Fast selection of best-fit models of protein evolution
-
Darriba, D., Taboada, G. L., Doallo, R. and Posada, D. (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27, 1164-1165.
-
(2011)
Bioinformatics
, vol.27
, pp. 1164-1165
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
24
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
25
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
26
-
-
83055173304
-
The first identification of lysine malonylation substrates and its regulatory enzyme
-
Peng, C., Lu, Z., Xie, Z., Cheng, Z., Chen, Y., Tan, M., Luo, H., Zhang, Y., He, W., Yang, K. et al. (2011) The first identification of lysine malonylation substrates and its regulatory enzyme. Mol. Cell. Proteomics, 10, M111 012658.
-
(2011)
Mol. Cell. Proteomics
, vol.10
, pp. M111-012658
-
-
Peng, C.1
Lu, Z.2
Xie, Z.3
Cheng, Z.4
Chen, Y.5
Tan, M.6
Luo, H.7
Zhang, Y.8
He, W.9
Yang, K.10
-
27
-
-
81055122671
-
Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase
-
Du, J., Zhou, Y., Su, X., Yu, J. J., Khan, S., Jiang, H., Kim, J., Woo, J., Kim, J. H., Choi, B. H. et al. (2011) Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science, 334, 806-809.
-
(2011)
Science
, vol.334
, pp. 806-809
-
-
Du, J.1
Zhou, Y.2
Su, X.3
Yu, J.J.4
Khan, S.5
Jiang, H.6
Kim, J.7
Woo, J.8
Kim, J.H.9
Choi, B.H.10
-
28
-
-
84890673317
-
Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli
-
Colak, G., Xie, Z., Zhu, A. Y., Dai, L., Lu, Z., Zhang, Y., Wan, X., Chen, Y., Cha, Y. H., Lin, H. et al. (2013) Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol. Cell. Proteomics, 12, 3509-3520.
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 3509-3520
-
-
Colak, G.1
Xie, Z.2
Zhu, A.Y.3
Dai, L.4
Lu, Z.5
Zhang, Y.6
Wan, X.7
Chen, Y.8
Cha, Y.H.9
Lin, H.10
-
29
-
-
84862907582
-
Plasmodium falciparum Sir2A preferentially hydrolyzes medium and long chain fatty acyl lysine
-
Zhu, A. Y., Zhou, Y., Khan, S., Deitsch, K. W., Hao, Q. and Lin, H. (2011) Plasmodium falciparum Sir2A preferentially hydrolyzes medium and long chain fatty acyl lysine. ACS Chem. Biol., 7, 155-159.
-
(2011)
ACS Chem. Biol.
, vol.7
, pp. 155-159
-
-
Zhu, A.Y.1
Zhou, Y.2
Khan, S.3
Deitsch, K.W.4
Hao, Q.5
Lin, H.6
-
30
-
-
0033887456
-
Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins
-
Frye, R. A. (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res. Commun., 273, 793-798.
-
(2000)
Biochem. Biophys. Res. Commun.
, vol.273
, pp. 793-798
-
-
Frye, R.A.1
-
31
-
-
84906540969
-
Expert curation in UniProtKB: A case study on dealing with conflicting and erroneous data
-
Poux, S., Magrane, M., Arighi, C. N., Bridge, A., O'Donovan, C. and Laiho, K. (2014) Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database (Oxford), bau016.
-
(2014)
Database (Oxford)
, pp. bau016
-
-
Poux, S.1
Magrane, M.2
Arighi, C.N.3
Bridge, A.4
O'Donovan, C.5
Laiho, K.6
-
32
-
-
0041955200
-
Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase
-
Bapteste, E., Moreira, D. and Philippe, H. (2003) Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase. Gene, 318, 185-191.
-
(2003)
Gene
, vol.318
, pp. 185-191
-
-
Bapteste, E.1
Moreira, D.2
Philippe, H.3
-
33
-
-
0036094071
-
The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi
-
Moore, S. A., Ronimus, R. S., Roberson, R. S. and Morgan, H. W. (2002) The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi. Structure, 10, 659-671.
-
(2002)
Structure
, vol.10
, pp. 659-671
-
-
Moore, S.A.1
Ronimus, R.S.2
Roberson, R.S.3
Morgan, H.W.4
-
34
-
-
0034680770
-
The primordial high energy compound: ATP or inorganic pyrophosphate?
-
Chi, A. and Kemp, R. G. (2000) The primordial high energy compound: ATP or inorganic pyrophosphate? J. Biol. Chem., 275, 35677-35679.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 35677-35679
-
-
Chi, A.1
Kemp, R.G.2
-
35
-
-
0034751692
-
Presence of prokaryotic and eukaryotic species in all subgroups of the PP (i)-dependent group II phosphofructokinase protein family
-
Muller, M., Lee, J. A., Gordon, P., Gaasterland, T. and Sensen, C. W. (2001) Presence of prokaryotic and eukaryotic species in all subgroups of the PP (i)-dependent group II phosphofructokinase protein family. J. Bacteriol., 183, 6714-6716.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 6714-6716
-
-
Muller, M.1
Lee, J.A.2
Gordon, P.3
Gaasterland, T.4
Sensen, C.W.5
-
36
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G. et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236-1240.
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
McWilliam, H.7
Maslen, J.8
Mitchell, A.9
Nuka, G.10
-
37
-
-
84858602406
-
InterPro in 2011: New developments in the family and domain prediction database
-
Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T. K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D306-D312
-
-
Hunter, S.1
Jones, P.2
Mitchell, A.3
Apweiler, R.4
Attwood, T.K.5
Bateman, A.6
Bernard, T.7
Binns, D.8
Bork, P.9
Burge, S.10
-
38
-
-
84886395049
-
Pfsearchv3: A code acceleration and heuristic to search PROSITE profiles
-
Schuepbach, T., Pagni, M., Bridge, A., Bougueleret, L., Xenarios, I. and Cerutti, L. (2013) pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinformatics, 29, 1215-1217.
-
(2013)
Bioinformatics
, vol.29
, pp. 1215-1217
-
-
Schuepbach, T.1
Pagni, M.2
Bridge, A.3
Bougueleret, L.4
Xenarios, I.5
Cerutti, L.6
|