-
1
-
-
0032431024
-
Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics
-
Zarembinski T.I., Hung L.W., Mueller-Dieckmann H.J., Kim K.K., Yokota H., Kim R., Kim S.H. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc. Natl. Acad. Sci. U.S.A. 95:1998;15189-15193.
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 15189-15193
-
-
Zarembinski, T.I.1
Hung, L.W.2
Mueller-Dieckmann, H.J.3
Kim, K.K.4
Yokota, H.5
Kim, R.6
Kim, S.H.7
-
2
-
-
0031928367
-
Shining a light on structural genomics
-
Kim S.H. Shining a light on structural genomics. Nature Struct. Biol. 5:1998;643-645.
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 643-645
-
-
Kim, S.H.1
-
3
-
-
0032104477
-
How far divergent evolution goes in proteins
-
Murzin A.G. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8:1998;380-387.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 380-387
-
-
Murzin, A.G.1
-
4
-
-
0036228122
-
Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics
-
Aloy P., Oliva B., Querol E., Aviles F.X., Russell R.B. Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. Protein Sci. 11:2002;1101-1116.
-
(2002)
Protein Sci.
, vol.11
, pp. 1101-1116
-
-
Aloy, P.1
Oliva, B.2
Querol, E.3
Aviles, F.X.4
Russell, R.B.5
-
5
-
-
17444398048
-
Structure-based identification of a novel NTPase from Methanococcus jannaschii
-
Hwang K.Y., Chung J.H., Kim S.H., Han Y.S., Cho Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat. Struct. Biol. 6:1999;691-696.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 691-696
-
-
Hwang, K.Y.1
Chung, J.H.2
Kim, S.H.3
Han, Y.S.4
Cho, Y.5
-
6
-
-
0032787396
-
Implication of tubby proteins as transcription factors by structure-based functional analysis
-
Boggon T.J., Shan W.S., Santagata S., Myers S.C., Shapiro L. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science. 286:1999;2119-2125.
-
(1999)
Science
, vol.286
, pp. 2119-2125
-
-
Boggon, T.J.1
Shan, W.S.2
Santagata, S.3
Myers, S.C.4
Shapiro, L.5
-
7
-
-
0036584359
-
Timeline: The march of structural biology
-
Campbell I.D. Timeline: the march of structural biology. Nat. Rev. Mol. Cell Biol. 3:2002;377-381.
-
(2002)
Nat. Rev. Mol. Cell Biol.
, vol.3
, pp. 377-381
-
-
Campbell, I.D.1
-
9
-
-
0033757870
-
Structural genomics in North America
-
Terwilliger T.C. Structural genomics in North America. Nat. Struct. Biol. 7:2000;935-939.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 935-939
-
-
Terwilliger, T.C.1
-
10
-
-
0033739261
-
Structural genomics projects in Japan
-
Yokoyama S., Matsuo Y., Hirota H., Kigawa T., Shirouzu M., Kuroda Y., Kurumizaka H., Kawaguchi S., Ito Y., Shibata T.et al. Structural genomics projects in Japan. Prog. Biophys. Mol. Biol. 73:2000;363-376.
-
(2000)
Prog. Biophys. Mol. Biol.
, vol.73
, pp. 363-376
-
-
Yokoyama, S.1
Matsuo, Y.2
Hirota, H.3
Kigawa, T.4
Shirouzu, M.5
Kuroda, Y.6
Kurumizaka, H.7
Kawaguchi, S.8
Ito, Y.9
Shibata, T.10
-
11
-
-
0033757915
-
Structural genomics in Europe: Slow start, strong finish?
-
Heinemann U. Structural genomics in Europe: slow start, strong finish? Nat. Struct. Biol. 7:2000;940-942.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 940-942
-
-
Heinemann, U.1
-
12
-
-
0036922069
-
High throughput methods for gene cloning and expression
-
Dieckman L., Gu M., Stols L., Donnelly M.I., Collart F.R. High throughput methods for gene cloning and expression. Protein Expr. Purif. 25:2002;1-7.
-
(2002)
Protein Expr. Purif.
, vol.25
, pp. 1-7
-
-
Dieckman, L.1
Gu, M.2
Stols, L.3
Donnelly, M.I.4
Collart, F.R.5
-
13
-
-
0036713170
-
Engineering soluble proteins for structural genomics
-
Pedelacq J.D., Piltch E., Liong E.C., Berendzen J., Kim C.Y., Rho B.S., Park M.S., Terwilliger T.C., Waldo G.S. Engineering soluble proteins for structural genomics. Nat. Biotechnol. 20:2002;927-932.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 927-932
-
-
Pedelacq, J.D.1
Piltch, E.2
Liong, E.C.3
Berendzen, J.4
Kim, C.Y.5
Rho, B.S.6
Park, M.S.7
Terwilliger, T.C.8
Waldo, G.S.9
-
14
-
-
0036075170
-
Protein crystallization for genomics: Towards high-throughput optimization techniques
-
Chayen N.E., Saridakis E. Protein crystallization for genomics: towards high-throughput optimization techniques. Acta. Crystallogr. D. 58:2002;921-927.
-
(2002)
Acta. Crystallogr. D
, vol.58
, pp. 921-927
-
-
Chayen, N.E.1
Saridakis, E.2
-
15
-
-
0036137978
-
Fast drops: A high-throughput approach for setting up protein crystal screens
-
Villaseñor A., Sha M., Thana P., Browner M. Fast drops: a high-throughput approach for setting up protein crystal screens. BioTechniques. 32:2002;184-189.
-
(2002)
BioTechniques
, vol.32
, pp. 184-189
-
-
Villaseñor, A.1
Sha, M.2
Thana, P.3
Browner, M.4
-
16
-
-
0036793459
-
Automated mounting, centering and screening of crystals for high-throughput protein crystallography
-
Karain W.I., Bourenkov G.P., Blume H., Bartunik H.D. Automated mounting, centering and screening of crystals for high-throughput protein crystallography. Acta. Crystallogr. D. 58:2002;1519-1522.
-
(2002)
Acta. Crystallogr. D
, vol.58
, pp. 1519-1522
-
-
Karain, W.I.1
Bourenkov, G.P.2
Blume, H.3
Bartunik, H.D.4
-
17
-
-
0036795668
-
The TB structural genomics consortium crystallization facility: Towards automation from protein to electron density
-
Rupp B., Segelke B.W., Krupka H.I., Lekin T., Schafer J., Zemla A., Toppani D., Snell G., Earnest T. The TB structural genomics consortium crystallization facility: towards automation from protein to electron density. Acta. Crystallogr. D. 58:2002;1514-1518.
-
(2002)
Acta. Crystallogr. D
, vol.58
, pp. 1514-1518
-
-
Rupp, B.1
Segelke, B.W.2
Krupka, H.I.3
Lekin, T.4
Schafer, J.5
Zemla, A.6
Toppani, D.7
Snell, G.8
Earnest, T.9
-
18
-
-
0035846574
-
An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR
-
Bhavesh N.S., Panchal S.C., Hosur R.V. An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR. Biochemistry. 40:2001;14727-14735.
-
(2001)
Biochemistry
, vol.40
, pp. 14727-14735
-
-
Bhavesh, N.S.1
Panchal, S.C.2
Hosur, R.V.3
-
19
-
-
0033785799
-
Structural proteomics of an archaeon
-
Christendat D., Yee A., Dharamsi A., Kluger Y., Savchenko A., Cort J.R., Booth V., Mackereth C.D., Saridakis V., Ekiel I.et al. Structural proteomics of an archaeon. Nat. Struct. Biol. 7:2000;903-909.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 903-909
-
-
Christendat, D.1
Yee, A.2
Dharamsi, A.3
Kluger, Y.4
Savchenko, A.5
Cort, J.R.6
Booth, V.7
Mackereth, C.D.8
Saridakis, V.9
Ekiel, I.10
-
20
-
-
0037015054
-
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
-
This paper describes the high-throughput structural determination pipeline designed and implemented at Syrrx Corp. and the Joint Center for Structural Genomics. The results of the application of the pipeline to the proteome of thermophillic bacterium Thermotaga maritima are presented. Of the two structures used as examples of the final outputs of the pipeline, the structure of thymidylate synthase-complementing protein TM0423 is of particular interest. The presence of four FAD molecules in the central active site of the TM0423 tetramer suggests a flavin-dependent mechanism in the alternative thymidylate synthesis pathway.
-
Lesley S.A., Kuhn P., Godzik A., Deacon A.M., Mathews I., Kreusch A., Spraggon G., Klock H.E., McMullan D., Shin T.et al. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. U.S.A. 99:2002;11664-11669 This paper describes the high-throughput structural determination pipeline designed and implemented at Syrrx Corp. and the Joint Center for Structural Genomics. The results of the application of the pipeline to the proteome of thermophillic bacterium Thermotaga maritima are presented. Of the two structures used as examples of the final outputs of the pipeline, the structure of thymidylate synthase-complementing protein TM0423 is of particular interest. The presence of four FAD molecules in the central active site of the TM0423 tetramer suggests a flavin-dependent mechanism in the alternative thymidylate synthesis pathway.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 11664-11669
-
-
Lesley, S.A.1
Kuhn, P.2
Godzik, A.3
Deacon, A.M.4
Mathews, I.5
Kreusch, A.6
Spraggon, G.7
Klock, H.E.8
McMullan, D.9
Shin, T.10
-
21
-
-
0036600569
-
Structural genomics of proteins from conserved biochemical pathways and processes
-
Burley S.K., Bonanno J.B. Structural genomics of proteins from conserved biochemical pathways and processes. Curr. Opin. Struct. Biol. 12:2002;383-391.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 383-391
-
-
Burley, S.K.1
Bonanno, J.B.2
-
22
-
-
18244366113
-
An NMR approach to structural proteomics
-
This paper presents an NMR approach to structural genomics. The authors found 20% of the 500 small proteins that they have tested are amenable to NMR structure determination. They found that proteins from the thermophilic bacterium T. maritima had more well-behaved proteins on the basis of the expression, solubility and heteronuclear single quantum coherence (HSQC) results. By contrast, thermophilic properties of M. thermoautotrophicum proteins do not provide a significant advantage for structural genomics of small proteins using NMR. For a portion of 12 structures reported in the paper, putative functions have been inferred.
-
Yee A., Chang X., Pineda-Lucena A., Wu B., Semesi A., Le B., Ramelot T., Lee G.M., Bhattacharyya S., Gutierrez P.et al. An NMR approach to structural proteomics. Proc. Natl. Acad. Sci. U.S.A. 99:2002;1825-1830 This paper presents an NMR approach to structural genomics. The authors found 20% of the 500 small proteins that they have tested are amenable to NMR structure determination. They found that proteins from the thermophilic bacterium T. maritima had more well-behaved proteins on the basis of the expression, solubility and heteronuclear single quantum coherence (HSQC) results. By contrast, thermophilic properties of M. thermoautotrophicum proteins do not provide a significant advantage for structural genomics of small proteins using NMR. For a portion of 12 structures reported in the paper, putative functions have been inferred.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 1825-1830
-
-
Yee, A.1
Chang, X.2
Pineda-Lucena, A.3
Wu, B.4
Semesi, A.5
Le, B.6
Ramelot, T.7
Lee, G.M.8
Bhattacharyya, S.9
Gutierrez, P.10
-
23
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structure
-
Bernstein F.S., Koetzle T.F., Williams G.J., Meyer E.F. Jr., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structure. J. Mol. Biol. 112:1977;535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.S.1
Koetzle, T.F.2
Williams, G.J.3
Meyer E.F., Jr.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
24
-
-
0012763164
-
Crystal structure and functional analysis of a hypothetical protein, MJ0882, from Methanococcus jannaschii
-
in press
-
Huang L, Hung LW, Kim R, Kim, SH: Crystal structure and functional analysis of a hypothetical protein, MJ0882, from Methanococcus jannaschii. J Struct Funct Genomics 2003, in press.
-
(2003)
J Struct Funct Genomics
-
-
Huang, L.1
Hung, L.W.2
Kim, R.3
Kim, S.H.4
-
25
-
-
0035576364
-
Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine
-
Lim K., Zhang H., Tempczyk A., Bonander N., Toedt J., Howard A., Eisenstein E., Herzberg O. Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine. Proteins. 45:2001;397-407.
-
(2001)
Proteins
, vol.45
, pp. 397-407
-
-
Lim, K.1
Zhang, H.2
Tempczyk, A.3
Bonander, N.4
Toedt, J.5
Howard, A.6
Eisenstein, E.7
Herzberg, O.8
-
26
-
-
0036848698
-
The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase Is a methyltransferase
-
This paper describes an interesting example of structure-based reclassification of the enzymatic function of a protein. M. thermoautotrophicum MT0146/CbiT protein was originally annotated as precorrin-8w decarboxylase. The structure of MT0146 revealed an AdoMet-dependent methyltransferase fold and a bound AdoHcy. The authors suggest that all functional annotations in sequence and structure databases should cite the papers containing the primary experimental data establishing the functional assignment.
-
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 This paper describes an interesting example of structure-based reclassification of the enzymatic function of a protein. M. thermoautotrophicum MT0146/CbiT protein was originally annotated as precorrin-8w decarboxylase. The structure of MT0146 revealed an AdoMet-dependent methyltransferase fold and a bound AdoHcy. The authors suggest that all functional annotations in sequence and structure databases should cite the papers containing the primary experimental data establishing the functional assignment.
-
(2002)
Structure
, vol.10
, pp. 1475-1487
-
-
Keller, J.P.1
Smith, P.M.2
Benach, J.3
Christendat, D.4
DeTitta, G.T.5
Hunt, J.F.6
-
27
-
-
0034141555
-
Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution
-
Wang H., Boisvert D., Kim K.K., Kim R., Kim S.H. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution. EMBO J. 19:2000;317-323.
-
(2000)
EMBO J.
, vol.19
, pp. 317-323
-
-
Wang, H.1
Boisvert, D.2
Kim, K.K.3
Kim, R.4
Kim, S.H.5
-
28
-
-
0027536869
-
Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly
-
Tollervey D., Lehtonen H., Jansen R., Kern H., Hurt E.C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell. 72:1993;443-457.
-
(1993)
Cell
, vol.72
, pp. 443-457
-
-
Tollervey, D.1
Lehtonen, H.2
Jansen, R.3
Kern, H.4
Hurt, E.C.5
-
29
-
-
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
-
30
-
-
0037025191
-
An alternative flavin-dependent mechanism for thymidylate synthesis
-
This paper describes the biochemical assay that establishes the flavin-dependent mechanism for the alternative thymidylate synthesis pathway.
-
Myllykallio H., Lipowski G., Leduc D., Filee J., Forterre P., Liebl U. An alternative flavin-dependent mechanism for thymidylate synthesis. Science. 297:2002;105-107 This paper describes the biochemical assay that establishes the flavin-dependent mechanism for the alternative thymidylate synthesis pathway.
-
(2002)
Science
, vol.297
, pp. 105-107
-
-
Myllykallio, H.1
Lipowski, G.2
Leduc, D.3
Filee, J.4
Forterre, P.5
Liebl, U.6
-
31
-
-
0028871926
-
DALI: A network tool for protein structure comparison
-
Holm L., Sander C. DALI: a network tool for protein structure comparison. Trends Biochem. Sci. 20:1995;478-480.
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 478-480
-
-
Holm, L.1
Sander, C.2
-
32
-
-
0030068703
-
HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae
-
Noskov V.N.et al. HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae. Yeast. 12:1996;17-29.
-
(1996)
Yeast
, vol.12
, pp. 17-29
-
-
Noskov, V.N.1
-
33
-
-
0029785147
-
Mapping the protein universe
-
Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-603.
-
(1996)
Science
, vol.273
, pp. 595-603
-
-
Holm, L.1
Sander, C.2
-
34
-
-
0036408348
-
Bonanno JB: Structuring the universe of proteins
-
Burley S.K. Bonanno JB: Structuring the universe of proteins. Annu. Rev. Genomics. Hum. Genet. 3:2002;243-262.
-
(2002)
Annu. Rev. Genomics. Hum. Genet.
, vol.3
, pp. 243-262
-
-
Burley, S.K.1
-
35
-
-
0036643498
-
Targeting novel folds for structural genomics
-
McGuffin L.J., Jones D.T. Targeting novel folds for structural genomics. Proteins. 48:2002;44-52.
-
(2002)
Proteins
, vol.48
, pp. 44-52
-
-
McGuffin, L.J.1
Jones, D.T.2
-
36
-
-
0033768266
-
Target selection for structural genomics
-
Brenner S.E. Target selection for structural genomics. Nat. Struct. Biol. 7:2000;967-969.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 967-969
-
-
Brenner, S.E.1
-
37
-
-
0036228236
-
Knowledge-based selection of targets for structural genomics
-
Frishman D. Knowledge-based selection of targets for structural genomics. Protein Eng. 15:2002;169-183.
-
(2002)
Protein Eng.
, vol.15
, pp. 169-183
-
-
Frishman, D.1
-
38
-
-
0036322695
-
Target space for structural genomics revisited
-
Liu J., Rost B. Target space for structural genomics revisited. Bioinformatics. 18:2002;922-933.
-
(2002)
Bioinformatics
, vol.18
, pp. 922-933
-
-
Liu, J.1
Rost, B.2
-
40
-
-
0036330266
-
Selecting targets for structural determination by navigating in a graph of protein families
-
Portugaly E., Kifer I., Linial M. Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics. 18:2002;899-907.
-
(2002)
Bioinformatics
, vol.18
, pp. 899-907
-
-
Portugaly, E.1
Kifer, I.2
Linial, M.3
-
41
-
-
0033764251
-
Protein structure modeling for structural genomics
-
Sanchez R., Pieper U., Melo F., Eswar N., Marti-Renom M.A., Madhusudhan M.S., Mirkovic N., Sali A. Protein structure modeling for structural genomics. Nat. Struct. Biol. 7:2000;986-990.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 986-990
-
-
Sanchez, R.1
Pieper, U.2
Melo, F.3
Eswar, N.4
Marti-Renom, M.A.5
Madhusudhan, M.S.6
Mirkovic, N.7
Sali, A.8
-
42
-
-
0035109680
-
Functional and structural genomics using PEDANT
-
Frishman D., Albermann K., Hani J., Heumann K., Metanomski A., Zollner A., Mewes H.W. Functional and structural genomics using PEDANT. Bioinformatics. 17:2001;44-57 This paper describes the software design of PEDANT, one of the most comprehensive structure annotation servers available ( http://pedant.gsf.de/ ).
-
(2001)
Bioinformatics
, vol.17
, pp. 44-57
-
-
Frishman, D.1
Albermann, K.2
Hani, J.3
Heumann, K.4
Metanomski, A.5
Zollner, A.6
Mewes, H.W.7
-
43
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:2001;93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
44
-
-
0036468055
-
Structural proteomics: Developments in structure-to-function predictions
-
Norin M., Sundstrom M. Structural proteomics: developments in structure-to-function predictions. Trends Biotechnol. 20:2002;79-84.
-
(2002)
Trends Biotechnol.
, vol.20
, pp. 79-84
-
-
Norin, M.1
Sundstrom, M.2
|