-
1
-
-
34249073088
-
Structural and chemical profiling of human cytosolic sulfotransferases
-
doi: 10.1371/journal.pbio.0050097
-
Allai-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thonton J, Edwards AM, et al. 2007. Structural and chemical profiling of human cytosolic sulfotransferases. PLoS Biol 5: e97. doi: 10.1371/journal.pbio.0050097.
-
(2007)
PLoS Biol
, vol.5
-
-
Allai-Hassani, A.1
Pan, P.W.2
Dombrovski, L.3
Najmanovich, R.4
Tempel, W.5
Dong, A.6
Loppnau, P.7
Martin, F.8
Thonton, J.9
Edwards, A.M.10
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215: 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
-
3
-
-
58149187893
-
The GOA database in 2009 - An integrated Gene Ontology annotation resource
-
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. 2009. The GOA database in 2009 - an integrated Gene Ontology annotation resource. Nucleic Acids Res 37: D396-D403.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
4
-
-
0029835350
-
The MutT proteins or 'Nudix' hydrolases, a family of versatile, widely distributed, 'housecleaning' enzymes
-
DOI 10.1074/jbc.271.41.25059
-
Bessman MJ, Frick DN, O'Handley SF. 1996. The mutt proteins or "nudix"hydrolases, a family of versatile, widely distributed, "housecleaning"enzymes. J Biol Chem 271: 25059-25062. (Pubitemid 26337861)
-
(1996)
Journal of Biological Chemistry
, vol.271
, Issue.41
, pp. 25059-25062
-
-
Bessman, M.J.1
Frick, D.N.2
O'Handley, S.F.3
-
5
-
-
0032800522
-
Carbohydrate sulfotransferases: Mediators of extracellular communication
-
Bowman KG, Bertozzi CR. 1999. Carbohydrate sulfotransferases: mediators of extracellular communication. Chem Biol 6: 9-22.
-
(1999)
Chem Biol
, vol.6
, pp. 9-22
-
-
Bowman, K.G.1
Bertozzi, C.R.2
-
6
-
-
0033119399
-
Errors in genome annotation
-
DOI 10.1016/S0168-9525(99)01706-0, PII S0168952599017060
-
Brenner SE. 1999. Errors in genome annotation. Trends Genet 15: 132-133. (Pubitemid 29155430)
-
(1999)
Trends in Genetics
, vol.15
, Issue.4
, pp. 132-133
-
-
Brenner, S.E.1
-
7
-
-
0037151058
-
The structural motif in chondroitin sulfate for adhesion of Plasmodium falciparum-infected erythrocytes comprises disaccharide units of 4-O-sulfated and non-sulfated N-acetylgalactosamine linked to glucuronic acid
-
DOI 10.1074/jbc.M111401200
-
Chai W, Beeson JG, Lawson A. 2002. The structuralmotif in chondroitin sulfate for adhesion of Plasmodium falciparum-infected erythrocytes comprises disaccharide units of 4-O-sulfated and non-sulfated N-acetylgalactosamine linked to glucuronic acid. J Biol Chem277: 22438-22446. (Pubitemid 34967215)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.25
, pp. 22438-22446
-
-
Chai, W.1
Beeson, J.G.2
Lawson, A.M.3
-
8
-
-
0000228203
-
Amodel of evolutionary change in proteins
-
(ed.MODayhoff), National Biomedical Research Foundation, Bethesda, MD
-
Dayhoff MO,Schwartz RM, Orcutt BC. 1978. Amodel of evolutionary change in proteins. In Atlas of protein sequence and structure (ed.MODayhoff), pp. 345-352. National Biomedical Research Foundation, Bethesda, MD.
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
9
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763. (Pubitemid 28552108)
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
10
-
-
0031976258
-
Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
-
Eisen JA. 1998. Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163-167. (Pubitemid 28177226)
-
(1998)
Genome Research
, vol.8
, Issue.3
, pp. 163-167
-
-
Eisen, J.A.1
-
11
-
-
0032786233
-
A phylogenomics study of DNA repair genes, proteins, and processes
-
Eisen JA, Hanawalt PC. 1999. A phylogenomics study of DNA repair genes, proteins, and processes. Mutat Res 3: 171-213.
-
(1999)
Mutat Res
, vol.3
, pp. 171-213
-
-
Eisen, J.A.1
Hanawalt, P.C.2
-
12
-
-
33645310990
-
Protein molecular function prediction by Bayesian phylogenomics
-
doi: 10.1371/journal.pcbi.0010045
-
Engelhardt BE, Jordan MI, Muratore K, Brenner SE. 2005. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1: e45. doi: 10.1371/journal.pcbi.0010045.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Engelhardt, B.E.1
Jordan, M.I.2
Muratore, K.3
Brenner, S.E.4
-
14
-
-
0000122573
-
Phylip - PHYLogeny Inference Package
-
version 3.2
-
Felsenstein J. 1989. Phylip - PHYLogeny Inference Package (version 3.2). Cladistics 5: 164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
15
-
-
75549090603
-
The Pfam protein families database
-
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. 2010. The Pfam protein families database. Nucleic Acids Res 38: D211-D222.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
-
16
-
-
0032229196
-
Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement, and operon disruption
-
Galperin MY, Koonin EV. 1998. Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption. In Silico Biol 1: 55-67.
-
(1998)
In Silico Biol
, vol.1
, pp. 55-67
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
17
-
-
0004012196
-
-
2nd ed. Chapman & Hall/CRC, Boca Raton, FL
-
Gelman A, Carlin JB, Stern HS, Rubin DB. 2003. Bayesian data analysis, 2nd ed. Chapman & Hall/CRC, Boca Raton, FL.
-
(2003)
Bayesian Data Analysis
-
-
Gelman, A.1
Carlin, J.B.2
Stern, H.S.3
Rubin, D.B.4
-
18
-
-
75849158230
-
The Gene Ontology in 2010: Extensions and refinements
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium. 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38: D331-D335.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
-
19
-
-
34748833440
-
Sulfated steroids as endogenous neuromodulators
-
DOI 10.1016/j.pbb.2006.07.031, PII S0091305706002413
-
Gibbs TT, Russek SJ, Farb DH. 2006. Sulfated steroids as endogenous neuromodulators. Pharmacol Biochem Behav 84: 555-567. (Pubitemid 350061235)
-
(2006)
Pharmacology Biochemistry and Behavior
, vol.84
, Issue.4
, pp. 555-567
-
-
Gibbs, T.T.1
Russek, S.J.2
Farb, D.H.3
-
20
-
-
33744471931
-
Enhanced automated function prediction using distantly related sequences and contextual association by PFP
-
DOI 10.1110/ps.062153506
-
Hawkins T, Luban S, Kihara D. 2006. Enhanced automated function prediction using distantly related sequences and contextual associations by PFP. Protein Sci 15: 1550-1556. (Pubitemid 43800030)
-
(2006)
Protein Science
, vol.15
, Issue.6
, pp. 1550-1556
-
-
Hawkins, T.1
Luban, S.2
Kihara, D.3
-
21
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci 89: 10915-10919.
-
(1992)
Proc Natl Acad Sci
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
22
-
-
0027522193
-
A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses
-
Koonin EV. 1993. A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes, and viruses. Nucleic Acids Res 21: 4847. doi: 10.1093/nar/21.20.4847. (Pubitemid 23312768)
-
(1993)
Nucleic Acids Research
, vol.21
, Issue.20
, pp. 4847
-
-
Koonin, E.V.1
-
23
-
-
48449088976
-
FFPred: An integrated feature-based function prediction server for vertebrate proteomes
-
Lobley AE, Nugent T, Orengo CA, Jones DT. 2008. FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 36: W297-W302.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Lobley, A.E.1
Nugent, T.2
Orengo, C.A.3
Jones, D.T.4
-
24
-
-
30744470374
-
The Nudix hydrolase superfamily
-
DOI 10.1007/s00018-005-5386-7
-
McLennan AG. 2006. The Nudix hydrolase superfamily. Cell Mol Life Sci 63: 123-143. (Pubitemid 43100287)
-
(2006)
Cellular and Molecular Life Sciences
, vol.63
, Issue.2
, pp. 123-143
-
-
McLennan, A.G.1
-
25
-
-
9744224380
-
Structures and mechanisms of Nudix hydrolases
-
DOI 10.1016/j.abb.2004.08.017, PII S0003986104004667
-
Mildvan AS, Xia Z, Azurmendi HF, Saraswat V, Legler PM, Massiah MA, Gabelli SB, Bianchet MA, Kang L-W, Amzel LM. 2005. Structures and mechanisms of Nudix hydrolases. Arch Biochem Biophys 433: 129-143. (Pubitemid 39586588)
-
(2005)
Archives of Biochemistry and Biophysics
, vol.433
, Issue.1
, pp. 129-143
-
-
Mildvan, A.S.1
Xia, Z.2
Azurmendi, H.F.3
Saraswat, V.4
Legler, P.M.5
Massiah, M.A.6
Gabelli, S.B.7
Bianchet, M.A.8
Kang, L.-W.9
Amzel, L.M.10
-
26
-
-
2342644032
-
Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes
-
DOI 10.1016/j.jmb.2004.01.065, PII S0022283604003067
-
Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu WL, Bessman MJ, Brenner SE, Holbrook SR. 2004. Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. J Mol Biol 339: 103-116. (Pubitemid 38569692)
-
(2004)
Journal of Molecular Biology
, vol.339
, Issue.1
, pp. 103-116
-
-
Ranatunga, W.1
Hill, E.E.2
Mooster, J.L.3
Holbrook, E.L.4
Schulze-Gahmen, U.5
Xu, W.6
Bessman, M.J.7
Brenner, S.E.8
Holbrook, S.R.9
-
27
-
-
74549221383
-
Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
-
doi: 10.1371/journal.pcbi.1000605
-
Schnoes AM, Brown SD, Dodevski I, Babbitt PC. 2009. Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5: e1000605. doi: 10.1371/journal.pcbi.1000605.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Schnoes, A.M.1
Brown, S.D.2
Dodevski, I.3
Babbitt, P.C.4
-
29
-
-
0036173130
-
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
-
Storm CE, Sonnhammer EL. 2002. Automated ortholog inference from phylogenetic trees and calculation of ortholog reliability. Bioinformatics 18: 92-99. (Pubitemid 34145036)
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. 92-99
-
-
Storm, C.E.V.1
Sonnhammer, E.L.L.2
-
31
-
-
33646591222
-
There is no universal molecular clock for invertebrates, but rate variation does not scale with body size
-
DOI 10.1073/pnas.0510251103
-
Thomas JA, Welch JJ, Wollfit M, Bromhan L. 2006. There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proc Natl Acad Sci 103: 7366-7371. (Pubitemid 43727839)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.19
, pp. 7366-7371
-
-
Thomas, J.A.1
Welch, J.J.2
Woolfit, M.3
Bromham, L.4
-
32
-
-
75849153303
-
The Universal Protein Resource (UniProt) in 2010
-
The UniProt Consortium
-
The UniProt Consortium. 2010. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38: D142-D148.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
-
33
-
-
40749111548
-
ConFunc - Functional annotation in the twilight zone
-
DOI 10.1093/bioinformatics/btn037
-
Wass MN, Sternberg MJE. 2008. ConFunc - functional annotation in the twilight zone. Bioinformatics 24: 798-806. (Pubitemid 351386918)
-
(2008)
Bioinformatics
, vol.24
, Issue.6
, pp. 798-806
-
-
Wass, M.N.1
Sternberg, M.J.E.2
-
34
-
-
33644878388
-
Pandit: An evolution-centric database of protein and associated nucleotide domains with inferred trees
-
Whelan S, de Bakker PIW, Quevillon E, Rodriguez N, Goldman N. 2006. Pandit: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res 34: D327-D331.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Whelan, S.1
De Bakker, P.I.W.2
Quevillon, E.3
Rodriguez, N.4
Goldman, N.5
-
35
-
-
0034791426
-
A simple algorithm to infer gene duplication and speciation events on a gene tree
-
Zmasek CM, Eddy SR. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828. (Pubitemid 32970480)
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 821-828
-
-
Zmasek, C.M.1
Eddy, S.R.2
|