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Applying motif and profile searches
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0029919635
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The SBASE protein domain library, release 4.0: A collection of annotated protein sequence sgments
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Searching protein structure databases has come of age
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0028953803
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Ready for a motif submission? A proposed checklist
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Bork P, Ouzounis C, McEntyre J: Ready for a motif submission? A proposed checklist Trends Biochem Sci 1995, 20:104. This paper provides a draft of a minimal set of rules making a new motif admissible.
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Trends Biochem Sci
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Bork, P.1
Ouzounis, C.2
McEntyre, J.3
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Issues in searching molecular sequence databases
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Altschul SF, Boguski MS, Gish W, Wootton JC: Issues in searching molecular sequence databases. Nat Genet 1994, 6:119-129.
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Some useful statistical properties of position-dependent weight matrices
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Claverie JM: Some useful statistical properties of position-dependent weight matrices. Comput Chem 1994, 18:287-294.
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Detecting patterns in protein sequences
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Discovering active motifs in sets of related proteins sequences and using them for classification
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Wang JT, Marr TG, Shasha D, Shapiro BA, Chirn GW: Discovering active motifs in sets of related proteins sequences and using them for classification. Nucleic Acids Res 1994, 22:2769-2775.
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Wang, J.T.1
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Prediction of zinc finger DNA binding protein
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Nakata K: Prediction of zinc finger DNA binding protein. CABIOS 1995, 11:125-131.
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Nakata, K.1
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0028968319
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Finding flexible patterns in a text: An application to three-dimensional molecular matching
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Sagot MF, Viari A, Pothier J, Soldano H: Finding flexible patterns in a text: an application to three-dimensional molecular matching. CABIOS 1995, 11:59-70.
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17
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0028091659
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Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
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Tatusov RL, Altschul SF, Koonin EV: Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci USA 1994, 91:12091-12095.
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Tatusov, R.L.1
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0029144601
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Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
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Neuwald AF, Liu JS, Lawrence CE: Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 1995, 4:1618-1632.
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Protein Sci
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Neuwald, A.F.1
Liu, J.S.2
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0029185456
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Identification of protein motifs using conserved amino acid properties and partitioning techniques
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Wu TD, Brutlag DL: Identification of protein motifs using conserved amino acid properties and partitioning techniques. Intelligent Systems in Molecular Biology 1995, 3:402-410.
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Intelligent Systems in Molecular Biology
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Wu, T.D.1
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21
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0029559311
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Sequence similarity analysis of Escherichia coli proteins: Functional and evolutionary implications
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Koonin EV, Tatusov RL, Rudd KE: Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc Natl Acad Sci USA 1995, 92:11921-11925. A prototype of a genome-scale sequence analysis study that includes motif analysis as an integral component, with a specialized motif library being one of the results.
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Proc Natl Acad Sci USA
, vol.92
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Koonin, E.V.1
Tatusov, R.L.2
Rudd, K.E.3
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23
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0028938731
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Conservation of a common motif in enzymes catalysing ADP-ribose transfer
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Takada T, lida K, Moss J: Conservation of a common motif in enzymes catalysing ADP-ribose transfer. J Biol Chem 1995, 270:541-544.
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J Biol Chem
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Takada, T.1
Lida, K.2
Moss, J.3
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24
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0029026444
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A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development
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Mushegian AR, Koonin EV: A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development Protein Sci 1995, 4:1243-1244.
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Protein Sci
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Mushegian, A.R.1
Koonin, E.V.2
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25
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0029084226
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The cytidylyltransferase superfamily: Identification of the nucleotide-binding site and fold prediction
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Bork P, Holm L, Koonin EV, Sander C: The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction. Proteins 1995, 22:259-266. An example of the extension of a motif initially derived by sequence analysis into the sequence-structure comparison area, resulting in a non-trivial connection between various nucleotidyltransferases and aminoacyl MRNA synthetases.
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(1995)
Proteins
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, pp. 259-266
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Bork, P.1
Holm, L.2
Koonin, E.V.3
Sander, C.4
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26
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0029360327
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DNA polymerase b belongs to an ancient nucleotidyltransferase superfamily
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Holm L, Sander C: DNA polymerase b belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci 1995, 20:345-347. An example of a successful transfer of a discovered structural similarity to a sequence motif, resulting in the detection of a connection between DNA polymerases and nucleotidyl transferases that may have far reaching biological implications.
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(1995)
Trends Biochem Sci
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, pp. 345-347
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Holm, L.1
Sander, C.2
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27
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0028969335
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Evolutionary link between glycogen phosphorylase and a DNa modifying enzyme
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Holm L, Sander C: Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme. EMBO J 1995, 14:1287-1293.
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EMBO J
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Holm, L.1
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0028882241
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New protein functions in yeast chromosome VIII
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Ouzounis CA, Bork P, Casari G, Sander C: New protein functions in yeast chromosome VIII. Protein Sci 1996, 4:2426-2428.
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Protein Sci
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Ouzounis, C.A.1
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29
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0029144599
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Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor elF-2B subunits revealed by analysis of conserved sequence motifs
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Koonin EV: Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor elF-2B subunits revealed by analysis of conserved sequence motifs. Protein Sci 1995, 4:1608-1617. The paper describes the detection of a new motif, a dramatic modification of a known motif, and a known motif in an unexpected place in a single protein family.
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(1995)
Protein Sci
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Koonin, E.V.1
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30
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0028898556
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A new family of peptidyl-prolyl isomerases
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Rudd KE, Rouviere PE, Lazar S, Sofia H, Plunkett G, Koonin EV: A new family of peptidyl-prolyl isomerases. Trends Biochem Sci 1995, 20:12-14.
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Trends Biochem Sci
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Rudd, K.E.1
Rouviere, P.E.2
Lazar, S.3
Sofia, H.4
Plunkett, G.5
Koonin, E.V.6
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31
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0028931903
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Conserved sequence motifs in bacterial and bacteriophage chaperonins
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Koonin EV, Van der Vies SM: Conserved sequence motifs in bacterial and bacteriophage chaperonins. Trends Biochem Sci 1995, 20:14-15.
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Trends Biochem Sci
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Koonin, E.V.1
Van Der Vies, S.M.2
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32
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0028607524
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Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins
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Pietrokovski S: Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci 1994, 3:2340-2350.
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Protein Sci
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Pietrokovski, S.1
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33
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0028944672
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A protein splice-junction motif in hedgehog family proteins
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Koonin EV: A protein splice-junction motif in hedgehog family proteins. Trends Biochem Sci 1995, 20:141-142.
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(1995)
Trends Biochem Sci
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, pp. 141-142
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Koonin, E.V.1
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34
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0028948811
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The product of hedgehog autoproteolytic cleavage active in local and long-range signalling
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Porter JP, Von Kessler DP, Ekker SC, Young KE, Lee JJ, Moses K, Beachy PA: The product of hedgehog autoproteolytic cleavage active in local and long-range signalling. Nature 1995, 374:363-366.
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Nature
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Porter, J.P.1
Von Kessler, D.P.2
Ekker, S.C.3
Young, K.E.4
Lee, J.J.5
Moses, K.6
Beachy, P.A.7
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35
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0029048694
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Common sequence and structural features in the heat-shock factor and Ets families of DNA-binding domain
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Landsmann D, Wolffe AP: Common sequence and structural features in the heat-shock factor and Ets families of DNA-binding domain. Trends Biochem Sci 1995, 20:225-226. This paper demonstrates a biologically important relationship between two families of transcription factors that was not suspected before in spite of the availability of 3D structures for both of them.
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(1995)
Trends Biochem Sci
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, pp. 225-226
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Landsmann, D.1
Wolffe, A.P.2
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36
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0028812044
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The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1
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Aasland R, Stewart AF: The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1. Nucleic Acids Res 1995, 23:3163-31 73.
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Nucleic Acids Res
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Aasland, R.1
Stewart, A.F.2
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37
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0028802784
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The chromo superfamily: New members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin
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Koonin EV, Zhou S, Lucchesi JC: The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res 1995, 23:4229-4233.
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(1995)
Nucleic Acids Res
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Koonin, E.V.1
Zhou, S.2
Lucchesi, J.C.3
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38
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0029360452
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The FHa domain: A putative nuclear signalling domain found in protein kinases and transcription factors
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Hoffmann K, Bucher P: The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem Sci 1995, 20:347-349.
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(1995)
Trends Biochem Sci
, vol.20
, pp. 347-349
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Hoffmann, K.1
Bucher, P.2
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39
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0028850114
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Molecular cloning of a cDNa with a novel domain present in the tre-2 oncogene and the yeast cell cycle regulator BUB2 and cdc16
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Richardson PM, Zon Ll: Molecular cloning of a cDNA with a novel domain present in the tre-2 oncogene and the yeast cell cycle regulator BUB2 and cdc16. Oncogene 1995, 11:1139-1148.
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Oncogene
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Richardson, P.M.1
Zon, Ll.2
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40
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0028955712
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The Ran/TC4 GTPase-binding domain: Identification by expression cloning and characterization of a conserved sequence motif
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Beddow AL, Richards SA, Orem NR, Macara IG: The Ran/TC4 GTPase-binding domain: identification by expression cloning and characterization of a conserved sequence motif. Proc Natl Acad Sci USA 1995, 92:3328-3332.
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Proc Natl Acad Sci USA
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Beddow, A.L.1
Richards, S.A.2
Orem, N.R.3
Macara, I.G.4
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41
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0029127222
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A variety of DNA-binding and multimeric proteins contain the histone fold motif
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Baxevanis AD, Arents G, Moundrianakis EN, Landsman D: A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucleic Acids Res 1995, 23:2685-2691. This paper constitutes an example of a very thorough study of a widespread motif based on the systematic application of an iterative MoST. The study demonstrates both the power of this method and the need for cautious interpretation of the results using additional structural and biological criteria.
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(1995)
Nucleic Acids Res
, vol.23
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Baxevanis, A.D.1
Arents, G.2
Moundrianakis, E.N.3
Landsman, D.4
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42
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0028867087
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The histone fold: A ubiquitous architectural motif utilized in DNa compaction and protein dimerization
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Arents G, Moundrianakis EN: The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization. Proc Natl Acad Sci USA 1995, 92:111 70-11174.
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Proc Natl Acad Sci USA
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Arents, G.1
Moundrianakis, E.N.2
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43
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0029352111
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Identification of a common fold in the replication terminator proteins suggests a possible mode for DNa binding
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Swindells M: Identification of a common fold in the replication terminator proteins suggests a possible mode for DNA binding. Trends Biochem Sci 1995, 20:300-302.
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Trends Biochem Sci
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Swindells, M.1
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44
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0029032723
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Protein motifs 5. Zinc fingers
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Klug A, Schwabe JW: Protein motifs 5. Zinc fingers. FASEB J 1995, 9:597-604.
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FASEB J
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Klug, A.1
Schwabe, J.W.2
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45
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0028968330
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Cabeza, a Drosophila gene encoding a novel RNA-binding protein, shares homology with EWS and TLS, two genes involved in human sarcoma formation
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Stolow DT, Haynes SR: Cabeza, a Drosophila gene encoding a novel RNA-binding protein, shares homology with EWS and TLS, two genes involved in human sarcoma formation. Nucleic Acids Res 1995, 28:835-843.
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Nucleic Acids Res
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Stolow, D.T.1
Haynes, S.R.2
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46
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0029284998
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The APETALA2 domain is related to a novel type of DNA-binding domain
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Weigel D: The APETALA2 domain is related to a novel type of DNA-binding domain. Plant Cell 1995, 7:388-389.
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Plant Cell
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Weigel, D.1
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47
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0029049164
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A novel DNA-binding domain that may form a single zinc finger motif
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Yanagisawa S: A novel DNA-binding domain that may form a single zinc finger motif. Nucleic Acids Res 1995, 23:3403-3410.
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Nucleic Acids Res
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Yanagisawa, S.1
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48
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0028856787
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Presence of a new conserved domain in CART1, a novel member of the tumor necrosis factor receptor-associated protein family, which is expressed in breast carcinoma
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Regnier CH, Tomasetto C, Moog-Lutz C, Chenard MP, Wendling C, Basset P, Rio MC: Presence of a new conserved domain in CART1, a novel member of the tumor necrosis factor receptor-associated protein family, which is expressed in breast carcinoma. J Biol Chem 1995, 270:25715-25721. This paper describes the identification of a modified RING finger and a novel zinc finger-like domain as well as a domain shared with TRAF proteins.
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J Biol Chem
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, pp. 25715-25721
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Regnier, C.H.1
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Wendling, C.5
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Rio, M.C.7
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49
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0028861418
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The PHD finger: Implications for chromatin-mediated transcriptional regulation
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Aasland R, Gibson TJ, Stewart AF: The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci 1995, 20:56-58.
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Trends Biochem Sci
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Aasland, R.1
Gibson, T.J.2
Stewart, A.F.3
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51
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0028857948
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The leukemia-associated-protein (LAP) domain, a cysteine-rich motif, is present in a wide range of proteins, including MLL, AF10, and MLLT6 proteins
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Saha V, Chaplin T, Gregorini A, Ayton P, Young BD: The leukemia-associated-protein (LAP) domain, a cysteine-rich motif, is present in a wide range of proteins, including MLL, AF10, and MLLT6 proteins. Proc Natl Acad Sci USA 1995, 92:9737-9741.
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Proc Natl Acad Sci USA
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Saha, V.1
Chaplin, T.2
Gregorini, A.3
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Young, B.D.5
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52
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0029151566
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The Drosophila thrithorax proteins contain a novel variant of the nuclear receptor type DNa binding domain and an ancient conserved motif found in other chromosomal proteins
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Stassen MJ, Bailey D, Nelson S, Chinwalla, Harte PJ: The Drosophila thrithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins. Mech Dev 1995, 52:209-223.
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Mech Dev
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Stassen, M.J.1
Bailey, D.2
Nelson, S.3
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Harte, P.J.5
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53
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0029041105
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NMR solution structure of a dsRNa binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5
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Bycroft M, Grunert S, Murzin AG, Proctor M, St Johnston D: NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5. EMBO J 1995, 14:3563-3571.
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EMBO J
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Bycroft, M.1
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St Johnston, D.5
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54
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0029360415
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The death domain: A module shared by proteins with diverse functions
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Feinstein E, Wallach D, Boldin M, Vafolomeev E, Kimchi A:The death domain: a module shared by proteins with diverse functions. Trends Biochem Sci 1995, 20:342-345. A concise overview of the remarkable spread of the DEATH motif and its history.
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(1995)
Trends Biochem Sci
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, pp. 342-345
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Feinstein, E.1
Wallach, D.2
Boldin, M.3
Vafolomeev, E.4
Kimchi, A.5
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55
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0029583176
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Drosophila homologs of Baculovirus inhibitor of apoptosis proteins function to block cell death
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Hay AB, Wassarman DA, Rubin GM: Drosophila homologs of Baculovirus inhibitor of apoptosis proteins function to block cell death. Cell 1995, 83:1253-1262.
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Cell
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Hay, A.B.1
Wassarman, D.A.2
Rubin, G.M.3
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56
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0029595282
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The TNFR2-TRAF signaling complex contains two novel proteins related to baculoviral inhibitor of apoptosis proteins
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Rothe M, Pan M-G, Henzel WJ, Ayres TM, Goeddel DV. The TNFR2-TRAF signaling complex contains two novel proteins related to baculoviral inhibitor of apoptosis proteins. Cell 1995, 83:1243-1252.
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Cell
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Rothe, M.1
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57
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