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For: Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 2001;311:693-708. [PMID: 11518524 DOI: 10.1006/jmbi.2001.4912] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Widney KA, Phillips LC, Rusch LM, Copley SD. A cheater founds the winning lineages during evolution of a novel metabolic pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.26.634942. [PMID: 39990456 PMCID: PMC11844401 DOI: 10.1101/2025.01.26.634942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
2
Goldford JE, Smith HB, Longo LM, Wing BA, McGlynn SE. Primitive purine biosynthesis connects ancient geochemistry to modern metabolism. Nat Ecol Evol 2024;8:999-1009. [PMID: 38519634 DOI: 10.1038/s41559-024-02361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/06/2024] [Indexed: 03/25/2024]
3
Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB. Proc Natl Acad Sci U S A 2019;116:24164-24173. [PMID: 31712440 PMCID: PMC6883840 DOI: 10.1073/pnas.1915569116] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
4
Chaliotis A, Vlastaridis P, Mossialos D, Ibba M, Becker HD, Stathopoulos C, Amoutzias GD. The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res 2017;45:1059-1068. [PMID: 28180287 PMCID: PMC5388404 DOI: 10.1093/nar/gkw1182] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/20/2016] [Accepted: 11/16/2016] [Indexed: 12/15/2022]  Open
5
Martínez-Núñez MA, Rodríguez-Escamilla Z, Rodríguez-Vázquez K, Pérez-Rueda E. Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms. Life (Basel) 2017;7:life7030030. [PMID: 28703743 PMCID: PMC5617955 DOI: 10.3390/life7030030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023]  Open
6
Reconstruction and Application of Protein-Protein Interaction Network. Int J Mol Sci 2016;17:ijms17060907. [PMID: 27338356 PMCID: PMC4926441 DOI: 10.3390/ijms17060907] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 11/17/2022]  Open
7
Robinson JL, Bertolo RF. The Pediatric Methionine Requirement Should Incorporate Remethylation Potential and Transmethylation Demands. Adv Nutr 2016;7:523-34. [PMID: 27184279 PMCID: PMC4863267 DOI: 10.3945/an.115.010843] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
8
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. J Mol Biol 2015;428:253-267. [PMID: 26585402 PMCID: PMC4751976 DOI: 10.1016/j.jmb.2015.11.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/05/2015] [Accepted: 11/10/2015] [Indexed: 01/28/2023]
9
Das S, Dawson NL, Orengo CA. Diversity in protein domain superfamilies. Curr Opin Genet Dev 2015;35:40-9. [PMID: 26451979 PMCID: PMC4686048 DOI: 10.1016/j.gde.2015.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 01/25/2023]
10
Brown S, Babbitt P. Using the structure-function linkage database to characterize functional domains in enzymes. ACTA ACUST UNITED AC 2014;48:2.10.1-2.10.16. [PMID: 25501940 DOI: 10.1002/0471250953.bi0210s48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
11
Murakami Y, Kinoshita K, Kinjo AR, Nakamura H. Exhaustive comparison and classification of ligand-binding surfaces in proteins. Protein Sci 2013;22:1379-91. [PMID: 23934772 PMCID: PMC3795496 DOI: 10.1002/pro.2329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/29/2013] [Accepted: 08/05/2013] [Indexed: 12/03/2022]
12
Caetano-Anollés K, Caetano-Anollés G. Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism. PLoS One 2013;8:e59300. [PMID: 23516625 PMCID: PMC3596326 DOI: 10.1371/journal.pone.0059300] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 02/13/2013] [Indexed: 11/30/2022]  Open
13
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013;41:D808-15. [PMID: 23203871 PMCID: PMC3531103 DOI: 10.1093/nar/gks1094] [Citation(s) in RCA: 3337] [Impact Index Per Article: 278.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 10/15/2012] [Accepted: 10/18/2012] [Indexed: 12/12/2022]  Open
14
Suen S, Lu HHS, Yeang CH. Evolution of domain architectures and catalytic functions of enzymes in metabolic systems. Genome Biol Evol 2012;4:976-93. [PMID: 22936075 PMCID: PMC3468959 DOI: 10.1093/gbe/evs072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
15
Grassi L, Tramontano A. Horizontal and vertical growth of S. cerevisiae metabolic network. BMC Evol Biol 2011;11:301. [PMID: 21999464 PMCID: PMC3216907 DOI: 10.1186/1471-2148-11-301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 10/14/2011] [Indexed: 11/10/2022]  Open
16
Almonacid DE, Babbitt PC. Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol 2011;15:435-42. [PMID: 21489855 PMCID: PMC3551611 DOI: 10.1016/j.cbpa.2011.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 11/15/2022]
17
Lovelace LL, Cooper CL, Sodetz JM, Lebioda L. Structure of human C8 protein provides mechanistic insight into membrane pore formation by complement. J Biol Chem 2011;286:17585-92. [PMID: 21454577 PMCID: PMC3093833 DOI: 10.1074/jbc.m111.219766] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/23/2011] [Indexed: 11/06/2022]  Open
18
Khersonsky O, Malitsky S, Rogachev I, Tawfik DS. Role of Chemistry versus Substrate Binding in Recruiting Promiscuous Enzyme Functions. Biochemistry 2011;50:2683-90. [DOI: 10.1021/bi101763c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
19
Glasner ME, Gerlt JA, Babbitt PC. Mechanisms of protein evolution and their application to protein engineering. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2010;75:193-239, xii-xiii. [PMID: 17124868 DOI: 10.1002/9780471224464.ch3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
20
Almonacid DE, Yera ER, Mitchell JBO, Babbitt PC. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol 2010;6:e1000700. [PMID: 20300652 PMCID: PMC2837397 DOI: 10.1371/journal.pcbi.1000700] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/02/2010] [Indexed: 11/19/2022]  Open
21
Reid AJ, Ranea JA, Orengo CA. Comparative evolutionary analysis of protein complexes in E. coli and yeast. BMC Genomics 2010;11:79. [PMID: 20122144 PMCID: PMC2837643 DOI: 10.1186/1471-2164-11-79] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 02/01/2010] [Indexed: 11/17/2022]  Open
22
Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 2009;10:791-803. [PMID: 19851337 DOI: 10.1038/nrm2787] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
23
Chothia C, Gough J. Genomic and structural aspects of protein evolution. Biochem J 2009;419:15-28. [PMID: 19272021 DOI: 10.1042/bj20090122] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
24
Iwasaki W, Takagi T. Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages. PLoS Genet 2009;5:e1000402. [PMID: 19266023 PMCID: PMC2644373 DOI: 10.1371/journal.pgen.1000402] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 02/03/2009] [Indexed: 11/25/2022]  Open
25
The origin, evolution and structure of the protein world. Biochem J 2009;417:621-37. [PMID: 19133840 DOI: 10.1042/bj20082063] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
26
Trigo A, Valencia A, Cases I. Systemic approaches to biodegradation. FEMS Microbiol Rev 2009;33:98-108. [DOI: 10.1111/j.1574-6976.2008.00143.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
27
Lacroix V, Cottret L, Thébault P, Sagot MF. An introduction to metabolic networks and their structural analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2008;5:594-617. [PMID: 18989046 DOI: 10.1109/tcbb.2008.79] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
28
Caetano-Anollés G, Yafremava LS, Gee H, Caetano-Anollés D, Kim HS, Mittenthal JE. The origin and evolution of modern metabolism. Int J Biochem Cell Biol 2008;41:285-97. [PMID: 18790074 DOI: 10.1016/j.biocel.2008.08.022] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 08/09/2008] [Accepted: 08/11/2008] [Indexed: 10/21/2022]
29
Hernández-Montes G, Díaz-Mejía JJ, Pérez-Rueda E, Segovia L. The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. Genome Biol 2008;9:R95. [PMID: 18541022 PMCID: PMC2481427 DOI: 10.1186/gb-2008-9-6-r95] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 05/06/2008] [Accepted: 06/09/2008] [Indexed: 12/13/2022]  Open
30
Cygler M, Hung MN, Wagner J, Matte A. Bacterial structural genomics initiative: overview of methods and technologies applied to the process of structure determination. Methods Mol Biol 2008;426:537-559. [PMID: 18542889 DOI: 10.1007/978-1-60327-058-8_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
31
Díaz-Mejía JJ, Pérez-Rueda E, Segovia L. A network perspective on the evolution of metabolism by gene duplication. Genome Biol 2007;8:R26. [PMID: 17326820 PMCID: PMC1852415 DOI: 10.1186/gb-2007-8-2-r26] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 10/23/2006] [Accepted: 02/27/2007] [Indexed: 01/16/2023]  Open
32
Caetano-Anollés G, Kim HS, Mittenthal JE. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci U S A 2007;104:9358-63. [PMID: 17517598 PMCID: PMC1890499 DOI: 10.1073/pnas.0701214104] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
33
Kim HS, Mittenthal JE, Caetano-Anollés G. MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics 2006;7:351. [PMID: 16854231 PMCID: PMC1559654 DOI: 10.1186/1471-2105-7-351] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 07/19/2006] [Indexed: 11/13/2022]  Open
34
Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol 2006;360:228-50. [PMID: 16740275 DOI: 10.1016/j.jmb.2006.04.055] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 04/22/2006] [Accepted: 04/25/2006] [Indexed: 11/30/2022]
35
Pegg SCH, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry 2006;45:2545-55. [PMID: 16489747 DOI: 10.1021/bi052101l] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
36
Pereira-Leal JB, Levy ED, Teichmann SA. The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci 2006;361:507-17. [PMID: 16524839 PMCID: PMC1609335 DOI: 10.1098/rstb.2005.1807] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
37
Brown S, Babbitt P. Using the Structure-function Linkage Database to characterize functional domains in enzymes. CURRENT PROTOCOLS IN BIOINFORMATICS 2006;Chapter 2:Unit 2.10. [PMID: 18428763 DOI: 10.1002/0471250953.bi0210s13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
38
Pál C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 2005;37:1372-5. [PMID: 16311593 DOI: 10.1038/ng1686] [Citation(s) in RCA: 347] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 09/08/2005] [Indexed: 11/09/2022]
39
Song J, Bonner CA, Wolinsky M, Jensen RA. The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context. BMC Biol 2005;3:13. [PMID: 15888209 PMCID: PMC1173090 DOI: 10.1186/1741-7007-3-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2005] [Accepted: 05/12/2005] [Indexed: 11/10/2022]  Open
40
Pereira-Leal JB, Teichmann SA. Novel specificities emerge by stepwise duplication of functional modules. Genome Res 2005;15:552-9. [PMID: 15805495 PMCID: PMC1074369 DOI: 10.1101/gr.3102105] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Accepted: 01/26/2005] [Indexed: 11/24/2022]
41
Van Lanen SG, Reader JS, Swairjo MA, de Crécy-Lagard V, Lee B, Iwata-Reuyl D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A 2005;102:4264-9. [PMID: 15767583 PMCID: PMC555470 DOI: 10.1073/pnas.0408056102] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Indexed: 11/18/2022]  Open
42
Bonner C, Jensen R, Gander J, Keyhani N. A core catalytic domain of the TyrA protein family: arogenate dehydrogenase from Synechocystis. Biochem J 2005;382:279-91. [PMID: 15171683 PMCID: PMC1133941 DOI: 10.1042/bj20031809] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Revised: 05/11/2004] [Accepted: 06/01/2004] [Indexed: 11/17/2022]
43
Huynen MA, Gabaldón T, Snel B. Variation and evolution of biomolecular systems: Searching for functional relevance. FEBS Lett 2005;579:1839-45. [PMID: 15763561 DOI: 10.1016/j.febslet.2005.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 01/18/2005] [Accepted: 02/01/2005] [Indexed: 11/29/2022]
44
Liu J, Hegyi H, Acton TB, Montelione GT, Rost B. Automatic target selection for structural genomics on eukaryotes. Proteins 2004;56:188-200. [PMID: 15211504 DOI: 10.1002/prot.20012] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
45
Tsoka S, Ouzounis CA. Metabolic database systems for the analysis of genome-wide function. Biotechnol Bioeng 2004;84:750-5. [PMID: 14708115 DOI: 10.1002/bit.10881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
46
Apic G, Huber W, Teichmann SA. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. ACTA ACUST UNITED AC 2004;4:67-78. [PMID: 14649290 DOI: 10.1023/a:1026113408773] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
47
Meng EC, Polacco BJ, Babbitt PC. Superfamily active site templates. Proteins 2004;55:962-76. [PMID: 15146493 DOI: 10.1002/prot.20099] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Liu J, Rost B. CHOP proteins into structural domain-like fragments. Proteins 2004;55:678-88. [PMID: 15103630 DOI: 10.1002/prot.20095] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Light S, Kraulis P. Network analysis of metabolic enzyme evolution in Escherichia coli. BMC Bioinformatics 2004;5:15. [PMID: 15113413 PMCID: PMC394313 DOI: 10.1186/1471-2105-5-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Accepted: 02/18/2004] [Indexed: 11/10/2022]  Open
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Mizuta S, Munakata H, Aimaiti A, Oosawa K, Shimizu T. Evaluation of the color-coding method for searching tandem repeats in prokaryotic genomes. CHEM-BIO INFORMATICS JOURNAL 2004. [DOI: 10.1273/cbij.4.133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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