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For: Heger A, Holm L. Towards a covering set of protein family profiles. Prog Biophys Mol Biol 2001;73:321-37. [PMID: 11063778 DOI: 10.1016/s0079-6107(00)00013-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Zhang J, He W, Liang L, Sun B, Zhang Y. Study on the saltiness-enhancing mechanism of chicken-derived umami peptides by sensory evaluation and molecular docking to transmembrane channel-like protein 4 (TMC4). Food Res Int 2024;182:114139. [PMID: 38519171 DOI: 10.1016/j.foodres.2024.114139] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
2
Hao C, Elias JE, Lee PKH, Lam H. metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering. MICROBIOME 2023;11:176. [PMID: 37550758 PMCID: PMC10405559 DOI: 10.1186/s40168-023-01602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/18/2023] [Indexed: 08/09/2023]
3
Grahame DSA, Dupuis JH, Bryksa BC, Tanaka T, Yada RY. Comparative bioinformatic and structural analyses of pepsin and renin. Enzyme Microb Technol 2020;141:109632. [PMID: 33051007 DOI: 10.1016/j.enzmictec.2020.109632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/25/2020] [Accepted: 07/08/2020] [Indexed: 11/16/2022]
4
Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J Biol Chem 2019;294:10211-10235. [PMID: 31092555 PMCID: PMC6664185 DOI: 10.1074/jbc.ra119.007595] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Indexed: 12/20/2022]  Open
5
Watson AK, Lannes R, Pathmanathan JS, Méheust R, Karkar S, Colson P, Corel E, Lopez P, Bapteste E. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Methods Mol Biol 2019;1910:271-308. [PMID: 31278668 DOI: 10.1007/978-1-4939-9074-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
6
Krishnaraju RK, Hart TC, Schleyer TK. Comparative Genomics and Structure Prediction of Dental Matrix Proteins. Adv Dent Res 2016;17:100-3. [PMID: 15126218 DOI: 10.1177/154407370301700123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
7
Szilágyi SM, Szilágyi L. A fast hierarchical clustering algorithm for large-scale protein sequence data sets. Comput Biol Med 2014;48:94-101. [PMID: 24657908 DOI: 10.1016/j.compbiomed.2014.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/10/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022]
8
Seo JH, Park J, Kim EM, Kim J, Joo K, Lee J, Kim BG. Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm. Comput Biol Chem 2014;48:64-70. [PMID: 24378653 DOI: 10.1016/j.compbiolchem.2013.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/12/2013] [Accepted: 11/23/2013] [Indexed: 11/28/2022]
9
Devi PP, Adhikari S. Homology modeling and functional sites prediction of azoreductase enzyme from the cyanobacterium Nostoc sp. PCC7120. Interdiscip Sci 2013;4:310-8. [DOI: 10.1007/s12539-012-0140-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 05/02/2012] [Accepted: 07/30/2012] [Indexed: 10/27/2022]
10
Szilágyi L, Szilágyi SM. Efficient Markov clustering algorithm for protein sequence grouping. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013;2013:639-642. [PMID: 24109768 DOI: 10.1109/embc.2013.6609581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
11
Xu R, Wunsch DC. Clustering algorithms in biomedical research: a review. IEEE Rev Biomed Eng 2012;3:120-54. [PMID: 22275205 DOI: 10.1109/rbme.2010.2083647] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
12
Szilágyi L, Medvés L, Szilágyi SM. A modified Markov clustering approach to unsupervised classification of protein sequences. Neurocomputing 2010. [DOI: 10.1016/j.neucom.2010.02.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
13
Povolotskaya IS, Kondrashov FA. Sequence space and the ongoing expansion of the protein universe. Nature 2010;465:922-6. [PMID: 20485343 DOI: 10.1038/nature09105] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 04/19/2010] [Indexed: 11/09/2022]
14
Joseph JM, Durand D. Family classification without domain chaining. Bioinformatics 2009;25:i45-53. [PMID: 19478015 PMCID: PMC2687961 DOI: 10.1093/bioinformatics/btp207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
15
Han Y, Burnette JM, Wessler SR. TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic Acids Res 2009;37:e78. [PMID: 19429695 PMCID: PMC2699529 DOI: 10.1093/nar/gkp295] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Revised: 04/15/2009] [Accepted: 04/15/2009] [Indexed: 11/23/2022]  Open
16
Nakamura T, Kotani M, Tonozuka T, Ide A, Oguma K, Nishikawa A. Crystal Structure of the HA3 Subcomponent of Clostridium botulinum Type C Progenitor Toxin. J Mol Biol 2009;385:1193-206. [DOI: 10.1016/j.jmb.2008.11.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2008] [Revised: 11/15/2008] [Accepted: 11/19/2008] [Indexed: 11/30/2022]
17
Linial M. Fishing with (Proto)Net-a principled approach to protein target selection. Comp Funct Genomics 2008;4:542-8. [PMID: 18629007 PMCID: PMC2447289 DOI: 10.1002/cfg.328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2003] [Revised: 08/05/2003] [Accepted: 08/05/2003] [Indexed: 12/02/2022]  Open
18
Heger A, Korpelainen E, Hupponen T, Mattila K, Ollikainen V, Holm L. PairsDB atlas of protein sequence space. Nucleic Acids Res 2008;36:D276-80. [PMID: 17986464 PMCID: PMC2238971 DOI: 10.1093/nar/gkm879] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 09/28/2007] [Accepted: 10/01/2007] [Indexed: 11/12/2022]  Open
19
Heger A, Mallick S, Wilton C, Holm L. The global trace graph, a novel paradigm for searching protein sequence databases. Bioinformatics 2007;23:2361-7. [PMID: 17823134 DOI: 10.1093/bioinformatics/btm358] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
20
Langille MGI, Clark DV. Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles. Genomics 2007;90:334-43. [PMID: 17628393 DOI: 10.1016/j.ygeno.2007.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 05/26/2007] [Accepted: 06/05/2007] [Indexed: 01/12/2023]
21
Frenkel ZM, Trifonov EN. Walking through protein sequence space. J Theor Biol 2007;244:77-80. [DOI: 10.1016/j.jtbi.2006.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 07/03/2006] [Accepted: 07/26/2006] [Indexed: 11/30/2022]
22
Oberai A, Ihm Y, Kim S, Bowie JU. A limited universe of membrane protein families and folds. Protein Sci 2006;15:1723-34. [PMID: 16815920 PMCID: PMC2242558 DOI: 10.1110/ps.062109706] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/27/2006] [Accepted: 03/27/2006] [Indexed: 10/24/2022]
23
Paulsen I, von Haeseler A. INVHOGEN: a database of homologous invertebrate genes. Nucleic Acids Res 2006;34:D349-53. [PMID: 16381884 PMCID: PMC1347462 DOI: 10.1093/nar/gkj100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
24
Uchiyama I. Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res 2006;34:647-58. [PMID: 16436801 PMCID: PMC1351371 DOI: 10.1093/nar/gkj448] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
25
Krause A, Stoye J, Vingron M. Large scale hierarchical clustering of protein sequences. BMC Bioinformatics 2005;6:15. [PMID: 15663796 PMCID: PMC547898 DOI: 10.1186/1471-2105-6-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Accepted: 01/22/2005] [Indexed: 11/10/2022]  Open
26
Stevens FJ. Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: validation. J Mol Recognit 2005;18:139-49. [PMID: 15558595 DOI: 10.1002/jmr.721] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
27
Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW. BRAGI: linking and visualization of database information in a 3D viewer and modeling tool. Bioinformatics 2004;21:1291-3. [PMID: 15546941 DOI: 10.1093/bioinformatics/bti138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
28
Integral and differential form of the protein folding problem. Phys Life Rev 2004. [DOI: 10.1016/j.plrev.2004.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
29
Veeramachaneni V, Makałowski W. Visualizing sequence similarity of protein families. Genome Res 2004;14:1160-9. [PMID: 15140831 PMCID: PMC419794 DOI: 10.1101/gr.2079204] [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: 11/24/2022]
30
Ouzounis CA, Coulson RMR, Enright AJ, Kunin V, Pereira-Leal JB. Classification schemes for protein structure and function. Nat Rev Genet 2003;4:508-19. [PMID: 12838343 DOI: 10.1038/nrg1113] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
31
Heger A, Holm L. Exhaustive enumeration of protein domain families. J Mol Biol 2003;328:749-67. [PMID: 12706730 DOI: 10.1016/s0022-2836(03)00269-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
32
Copley RR, Ponting CP, Schultz J, Bork P. Sequence analysis of multidomain proteins: past perspectives and future directions. ADVANCES IN PROTEIN CHEMISTRY 2003;61:75-98. [PMID: 12461821 DOI: 10.1016/s0065-3233(02)61002-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
33
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002;30:1575-84. [PMID: 11917018 PMCID: PMC101833 DOI: 10.1093/nar/30.7.1575] [Citation(s) in RCA: 2415] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
34
Getz G, Vendruscolo M, Sachs D, Domany E. Automated assignment of SCOP and CATH protein structure classifications from FSSP scores. Proteins 2002;46:405-15. [PMID: 11835515 DOI: 10.1002/prot.1176] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
35
Blundell TL, Mizuguchi K. Structural genomics: an overview. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001;73:289-95. [PMID: 11063776 DOI: 10.1016/s0079-6107(00)00008-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
36
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2447210 DOI: 10.1002/cfg.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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