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1
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0035367880
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Determination of protein function, evolution and interactions by structural genomics
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Teichmann S.A., Murzin A.G., Chothia C. Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Struct. Biol. 11:2001;354-363.
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(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 354-363
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Teichmann, S.A.1
Murzin, A.G.2
Chothia, C.3
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2
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0036179451
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Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase
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Martinez-Cruz L.A., Dreyer M.K., Boisvert D.C., Yokota H., Martinez-Chantar M.L., Kim R., Kim S.H. Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure. 10:2002;195-204.
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(2002)
Structure
, vol.10
, pp. 195-204
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Martinez-Cruz, L.A.1
Dreyer, M.K.2
Boisvert, D.C.3
Yokota, H.4
Martinez-Chantar, M.L.5
Kim, R.6
Kim, S.H.7
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3
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0036848698
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The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase
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Keller J.P., Smith P.M., Benach J., Christendat D., deTitta G.T., Hunt J.F. The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure. 10:2002;1475-1487.
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(2002)
Structure
, vol.10
, pp. 1475-1487
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Keller, J.P.1
Smith, P.M.2
Benach, J.3
Christendat, D.4
DeTitta, G.T.5
Hunt, J.F.6
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4
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0036499628
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From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase
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Parsons J.F., Lim K., Tempczyk A., Krajewski W., Eisenstein E., Herzberg O. From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. Proteins. 46:2002;393-404.
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(2002)
Proteins
, vol.46
, pp. 393-404
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Parsons, J.F.1
Lim, K.2
Tempczyk, A.3
Krajewski, W.4
Eisenstein, E.5
Herzberg, O.6
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5
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0037062409
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Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus
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Shin D.H., Yokota H., Kim R., Kim S.H. Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc. Natl. Acad. Sci. USA. 99:2002;7980-7985.
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(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 7980-7985
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Shin, D.H.1
Yokota, H.2
Kim, R.3
Kim, S.H.4
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6
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0036513964
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Solution structure of the hypothetical protein MTH0637 from Methanobacterium thermoautotrophicum
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Pineda-Lucena A., Yi G.S., Chang X., Cort J.R., Kennedy M.A., Edwards A.M., Arrowsmith C.H. Solution structure of the hypothetical protein MTH0637 from Methanobacterium thermoautotrophicum. J. Biomol. NMR. 22:2002;291-294.
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J. Biomol. NMR
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, pp. 291-294
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Pineda-Lucena, A.1
Yi, G.S.2
Chang, X.3
Cort, J.R.4
Kennedy, M.A.5
Edwards, A.M.6
Arrowsmith, C.H.7
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7
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0037240909
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Structure of a yeast hypothetical protein selected by a structural genomics approach
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This paper is a good example of the difficulties of structure-based function annotation, especially when the structure has a widely distributed fold. In this case, the structure was revealed to be a typical TIM-barrel fold, one of the most frequently observed folds.
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Eswaramoorthy S., Gerchman S., Graziano V., Kycia H., Studier F.W., Swaminathan S. Structure of a yeast hypothetical protein selected by a structural genomics approach. Acta Crystallogr. D Biol. Crystallogr. 59:2003;127-135 This paper is a good example of the difficulties of structure-based function annotation, especially when the structure has a widely distributed fold. In this case, the structure was revealed to be a typical TIM-barrel fold, one of the most frequently observed folds.
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(2003)
Acta Crystallogr. D Biol. Crystallogr.
, vol.59
, pp. 127-135
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Eswaramoorthy, S.1
Gerchman, S.2
Graziano, V.3
Kycia, H.4
Studier, F.W.5
Swaminathan, S.6
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8
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0036102266
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The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum
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Christendat D., Saridakis V., Kim Y., Kumar P.A., Xu X., Semesi A., Joachimiak A., Arrowsmith C.H., Edwards A.M. The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum. Protein Sci. 11:2002;1409-1414.
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(2002)
Protein Sci.
, vol.11
, pp. 1409-1414
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Christendat, D.1
Saridakis, V.2
Kim, Y.3
Kumar, P.A.4
Xu, X.5
Semesi, A.6
Joachimiak, A.7
Arrowsmith, C.H.8
Edwards, A.M.9
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9
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0036606578
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NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli
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Pineda-Lucena A., Liao J., Wu B., Yee A., Cort J.R., Kennedy M.A., Edwards A.M., Arrowsmith C.H. NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli. Proteins. 47:2002;572-574.
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(2002)
Proteins
, vol.47
, pp. 572-574
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Pineda-Lucena, A.1
Liao, J.2
Wu, B.3
Yee, A.4
Cort, J.R.5
Kennedy, M.A.6
Edwards, A.M.7
Arrowsmith, C.H.8
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10
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0033757840
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From structure to function: Approaches and limitations
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Thornton J.M., Todd A.E., Milburn D., Borkakoti N., Orengo C.A. From structure to function: approaches and limitations. Nat. Struct. Biol. 7(suppl):2000;991-994.
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(2000)
Nat. Struct. Biol.
, vol.7
, Issue.SUPPL.
, pp. 991-994
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Thornton, J.M.1
Todd, A.E.2
Milburn, D.3
Borkakoti, N.4
Orengo, C.A.5
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11
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0037197857
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Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome
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Kihara D., Zhang Y., Lu H., Kolinski A., Skolnick J. Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc. Natl. Acad. Sci. USA. 99:2002;5993-5998.
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(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5993-5998
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Kihara, D.1
Zhang, Y.2
Lu, H.3
Kolinski, A.4
Skolnick, J.5
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12
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0036968925
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De novo prediction of three-dimensional structures for major protein families
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Bonneau R., Strauss C.E., Rohl C.A., Chivian D., Bradley P., Malmstrom L., Robertson T., Baker D. De novo prediction of three-dimensional structures for major protein families. J. Mol. Biol. 322:2002;65-78.
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J. Mol. Biol.
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, pp. 65-78
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Bonneau, R.1
Strauss, C.E.2
Rohl, C.A.3
Chivian, D.4
Bradley, P.5
Malmstrom, L.6
Robertson, T.7
Baker, D.8
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13
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0036087169
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SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
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Gough J., Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 30:2002;268-272.
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(2002)
Nucleic Acids Res.
, vol.30
, pp. 268-272
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Gough, J.1
Chothia, C.2
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14
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0036089481
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MODBASE, a database of annotated comparative protein structure models
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Pieper U., Eswar N., Stuart A.C., Ilyin V.A., Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30:2002;255-259.
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Nucleic Acids Res.
, vol.30
, pp. 255-259
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Pieper, U.1
Eswar, N.2
Stuart, A.C.3
Ilyin, V.A.4
Sali, A.5
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15
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0037250367
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Enlarged FAMSBASE: Protein 3D structure models of genome sequences for 41 species
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Yamaguchi A., Iwadate M., Suzuki E., Yura K., Kawakita S., Umeyama H., Go M. Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species. Nucleic Acids Res. 31:2003;463-468.
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Nucleic Acids Res.
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, pp. 463-468
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Yamaguchi, A.1
Iwadate, M.2
Suzuki, E.3
Yura, K.4
Kawakita, S.5
Umeyama, H.6
Go, M.7
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16
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0037162464
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Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds
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The number of proteins with disulfide bonds was estimated using a sequence/structure mapping method, a kind of sophisticated homology modelling technique. It was found that putative intracellular proteins from archaeal microbes contained an unexpectedly large number of disulfide bonds. Usually, intracellular proteins lack disulfide bonds due to the reducing environment in the cell, where disulfide bonds could destabilise the protein structure. This new finding is an excellent example of the use of structural information in terms of biological consequence.
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Mallick P., Boutz D.R., Eisenberg D., Yeates T.O. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl. Acad. Sci. USA. 99:2002;9679-9684 The number of proteins with disulfide bonds was estimated using a sequence/structure mapping method, a kind of sophisticated homology modelling technique. It was found that putative intracellular proteins from archaeal microbes contained an unexpectedly large number of disulfide bonds. Usually, intracellular proteins lack disulfide bonds due to the reducing environment in the cell, where disulfide bonds could destabilise the protein structure. This new finding is an excellent example of the use of structural information in terms of biological consequence.
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(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 9679-9684
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Mallick, P.1
Boutz, D.R.2
Eisenberg, D.3
Yeates, T.O.4
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17
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0036443972
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The constraints protein-protein interactions place on sequence divergence
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Teichmann S.A. The constraints protein-protein interactions place on sequence divergence. J. Mol. Biol. 324:2002;399-407.
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J. Mol. Biol.
, vol.324
, pp. 399-407
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Teichmann, S.A.1
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18
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0033617043
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Putative mechanism of natural transformation as deduced from genome data
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Yura K., Toh H., Go M. Putative mechanism of natural transformation as deduced from genome data. DNA Res. 6:1999;75-82.
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DNA Res.
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, pp. 75-82
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Yura, K.1
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19
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0036681416
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Scoring residue conservation
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Valdar W.S. Scoring residue conservation. Proteins. 48:2002;227-241.
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Proteins
, vol.48
, pp. 227-241
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Valdar, W.S.1
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0034308142
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Practical limits of function prediction
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Devos D., Valencia A. Practical limits of function prediction. Proteins. 41:2000;98-107.
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(2000)
Proteins
, vol.41
, pp. 98-107
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Devos, D.1
Valencia, A.2
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21
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0036776124
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Sequence and structural differences between enzyme and nonenzyme homologs
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By collecting pairs of homologous proteins that have completely different functions and whose structures have been solved, the authors tried to elucidate the possible pathways for proteins to gain a new function during evolution.
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Todd A.E., Orengo C.A., Thornton J.M. Sequence and structural differences between enzyme and nonenzyme homologs. Structure. 10:2002;1435-1451 By collecting pairs of homologous proteins that have completely different functions and whose structures have been solved, the authors tried to elucidate the possible pathways for proteins to gain a new function during evolution.
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(2002)
Structure
, vol.10
, pp. 1435-1451
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Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
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22
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0036384350
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One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
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Nagano N., Orengo C.A., Thornton J.M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321:2002;741-765.
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Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
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23
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0029913807
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An evolutionary trace method defines binding surfaces common to protein families
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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.
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Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
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24
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0036300444
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Structural clusters of evolutionary trace residues are statistically significant and common in proteins
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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.
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Madabushi, S.1
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Philippi, A.5
Sowa, M.E.6
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0035853280
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Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
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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.
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Landgraf, R.1
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Eisenberg, D.3
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0030821675
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Correlated mutations contain information about protein-protein interaction
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Pazos F., Helmer-Citterich M., Ausiello G., Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271:1997;511-523.
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Pazos, F.1
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0036435908
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Co-evolutionary analysis reveals insights into protein-protein interactions
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Goh C.S., Cohen F.E. Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324:2002;177-192.
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Goh, C.S.1
Cohen, F.E.2
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28
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0036568319
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In silico two-hybrid system for the selection of physically interacting protein pairs
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The concept of correlated mutations, originally proposed by Pazos et al. [26], was extended to predict protein-protein interactions, based on the assumption that mutations at the interface of interacting proteins should correlate. The authors tried to search for such correlated mutations by analysing pairs of multiple sequence alignments.
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Pazos F., Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins. 47:2002;219-227 The concept of correlated mutations, originally proposed by Pazos et al. [26], was extended to predict protein-protein interactions, based on the assumption that mutations at the interface of interacting proteins should correlate. The authors tried to search for such correlated mutations by analysing pairs of multiple sequence alignments.
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(2002)
Proteins
, vol.47
, pp. 219-227
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Pazos, F.1
Valencia, A.2
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29
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0037110589
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MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
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Lu L., Lu H., Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins. 49:2002;350-364.
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Proteins
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Lu, L.1
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0036384211
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Structural bases of stability-function tradeoffs in enzymes
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Beadle B.M., Shoichet B.K. Structural bases of stability-function tradeoffs in enzymes. J. Mol. Biol. 321:2002;285-296.
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0035965145
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Prediction of functionally important residues based solely on the computed energetics of protein structure
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Elcock A.H. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312:2001;885-896.
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Elcock, A.H.1
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0344405703
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Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation
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In this method, conserved sites identified by multiple sequence alignments were classified into functionally important residues and others, based on the assumption that functionally important amino acid residues could contribute to the destabilisation of the protein. The advantage of this method is that it uses a sophisticated 3D profile to evaluate the fitness of the amino acid residues in each site and also combines other structural features specifically found in the active sites of known proteins.
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Ota M., Kinoshita K., Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J. Mol. Biol. 327:2003;1053-1064 In this method, conserved sites identified by multiple sequence alignments were classified into functionally important residues and others, based on the assumption that functionally important amino acid residues could contribute to the destabilisation of the protein. The advantage of this method is that it uses a sophisticated 3D profile to evaluate the fitness of the amino acid residues in each site and also combines other structural features specifically found in the active sites of known proteins.
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J. Mol. Biol.
, vol.327
, pp. 1053-1064
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Ota, M.1
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0036968309
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Loopy proteins appear conserved in evolution
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Liu J., Tan H., Rost B. Loopy proteins appear conserved in evolution. J. Mol. Biol. 322:2002;53-64.
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0036893020
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Side-chain conformational entropy at protein-protein interfaces
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Although protein-protein interactions are frequently investigated by shape complementarity or electrostatic complementarity, the authors focused their attention on the dynamic property of the protein-protein interface in terms of sidechain conformational entropy. They found that a large fraction of the protein interface has less mobile sidechains than the rest of the protein surface.
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Cole C., Warwicker J. Side-chain conformational entropy at protein-protein interfaces. Protein Sci. 11:2002;2860-2870 Although protein-protein interactions are frequently investigated by shape complementarity or electrostatic complementarity, the authors focused their attention on the dynamic property of the protein-protein interface in terms of sidechain conformational entropy. They found that a large fraction of the protein interface has less mobile sidechains than the rest of the protein surface.
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Protein Sci.
, vol.11
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Cole, C.1
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0036406643
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A new method to detect related function among proteins independent of sequence and fold homology
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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.
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Schmitt, S.1
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0037070587
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Identification of ligand binding sites on proteins using a multi-scale approach
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Glick M., Robinson D.D., Grant G.H., Richards W.G. Identification of ligand binding sites on proteins using a multi-scale approach. J. Am. Chem. Soc. 124:2002;2337-2344.
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Glick, M.1
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0036084259
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Efficient docking of peptides to proteins without prior knowledge of the binding site
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Hetenyi C., van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci. 11:2002;1729-1737.
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0036169142
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LigBase: A database of families of aligned ligand binding sites in known protein sequences and structures
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Stuart A.C., Ilyin V.A., Sali A. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics. 18:2002;200-201.
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0036288284
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Identification of protein functions from a molecular surface database, eF-site
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Kinoshita K., Furui J., Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics. 2:2002;9-22.
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0030724039
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TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
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Wallace A.C., Borkakoti N., Thornton J.M. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6:1997;2308-2323.
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0032972775
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Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mononucleotide complexes
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Kinoshita K., Sadanami K., Kidera A., Go N. Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. Protein Eng. 12:1999;11-14.
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Go, N.4
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0036568353
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Classification of proteins based on the properties of the ligand-binding site: The case of adenine-binding proteins
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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. 47:2002;106-115.
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Proteins
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Cappello, V.1
Tramontano, A.2
Koch, U.3
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44
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0036893048
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Data mining the Protein Data Bank: Residue interactions
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A data-mining technique was applied to find the local atomic configurations that repeatedly appear in the active site and/or binding site of proteins; some new structural motifs were found. The author also described the construction of a template for the motifs and a search method with the template.
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Oldfield T.J. Data mining the Protein Data Bank: residue interactions. Proteins. 49:2002;510-528 A data-mining technique was applied to find the local atomic configurations that repeatedly appear in the active site and/or binding site of proteins; some new structural motifs were found. The author also described the construction of a template for the motifs and a search method with the template.
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(2002)
Proteins
, vol.49
, pp. 510-528
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Oldfield, T.J.1
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0036323965
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Ligand-induced changes in the binding sites of proteins
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Fradera X., De La Cruz X., Silva C.H., Gelpi J.L., Luque F.J., Orozco M. Ligand-induced changes in the binding sites of proteins. Bioinformatics. 18:2002;939-948.
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Bioinformatics
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Fradera, X.1
De La Cruz, X.2
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