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For: 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Castillo S, Barth D, Arvas M, Pakula TM, Pitkänen E, Blomberg P, Seppanen-Laakso T, Nygren H, Sivasiddarthan D, Penttilä M, Oja M. Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. BIOTECHNOLOGY FOR BIOFUELS 2016;9:252. [PMID: 27895706 PMCID: PMC5117618 DOI: 10.1186/s13068-016-0665-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/10/2016] [Indexed: 05/02/2023]
2
Kludas J, Arvas M, Castillo S, Pakula T, Oja M, Brouard C, Jäntti J, Penttilä M, Rousu J. Machine Learning of Protein Interactions in Fungal Secretory Pathways. PLoS One 2016;11:e0159302. [PMID: 27441920 PMCID: PMC4956264 DOI: 10.1371/journal.pone.0159302] [Citation(s) in RCA: 6] [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: 02/15/2016] [Accepted: 06/30/2016] [Indexed: 12/18/2022]  Open
3
Ma J, Wang S, Wang Z, Xu J. Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinformatics 2015;31:3506-13. [PMID: 26275894 DOI: 10.1093/bioinformatics/btv472] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 08/08/2015] [Indexed: 02/07/2023]  Open
4
Roston RL, Wang K, Kuhn LA, Benning C. Structural determinants allowing transferase activity in SENSITIVE TO FREEZING 2, classified as a family I glycosyl hydrolase. J Biol Chem 2014;289:26089-26106. [PMID: 25100720 DOI: 10.1074/jbc.m114.576694] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
5
Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, Oja M, Holm L, Penttilä M, Rousu J, Arvas M. Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species. PLoS Comput Biol 2014;10:e1003465. [PMID: 24516375 PMCID: PMC3916221 DOI: 10.1371/journal.pcbi.1003465] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 12/18/2013] [Indexed: 12/12/2022]  Open
6
Plyusnin I, Holm L. Comprehensive comparison of graph based multiple protein sequence alignment strategies. BMC Bioinformatics 2012;13:64. [PMID: 22540977 PMCID: PMC3375188 DOI: 10.1186/1471-2105-13-64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/29/2012] [Indexed: 12/03/2022]  Open
7
Söding J, Remmert M. Protein sequence comparison and fold recognition: progress and good-practice benchmarking. Curr Opin Struct Biol 2011;21:404-11. [PMID: 21458982 DOI: 10.1016/j.sbi.2011.03.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/01/2011] [Accepted: 03/09/2011] [Indexed: 11/26/2022]
8
Malysiak-Mrozek B, Mrozek D. An Improved Method for Protein Similarity Searching by Alignment of Fuzzy Energy Signatures. INT J COMPUT INT SYS 2011. [DOI: 10.1080/18756891.2011.9727765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]  Open
9
Melvin I, Weston J, Noble WS, Leslie C. Detecting remote evolutionary relationships among proteins by large-scale semantic embedding. PLoS Comput Biol 2011;7:e1001047. [PMID: 21298082 PMCID: PMC3029239 DOI: 10.1371/journal.pcbi.1001047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Accepted: 12/02/2010] [Indexed: 12/23/2022]  Open
10
Hasegawa H, Holm L. Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 2009;19:341-8. [PMID: 19481444 DOI: 10.1016/j.sbi.2009.04.003] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 04/16/2009] [Indexed: 11/30/2022]
11
Vertrees J, Wrabl JO, Hilser VJ. Energetic profiling of protein folds. Methods Enzymol 2009;455:299-327. [PMID: 19289211 PMCID: PMC5823608 DOI: 10.1016/s0076-6879(08)04211-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
12
Astikainen K, Holm L, Pitkänen E, Szedmak S, Rousu J. Towards structured output prediction of enzyme function. BMC Proc 2008;2 Suppl 4:S2. [PMID: 19091049 PMCID: PMC2654971 DOI: 10.1186/1753-6561-2-s4-s2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
13
Holm L, Kääriäinen S, Rosenström P, Schenkel A. Searching protein structure databases with DaliLite v.3. Bioinformatics 2008;24:2780-1. [PMID: 18818215 PMCID: PMC2639270 DOI: 10.1093/bioinformatics/btn507] [Citation(s) in RCA: 872] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
14
Pei J. Multiple protein sequence alignment. Curr Opin Struct Biol 2008;18:382-6. [PMID: 18485694 DOI: 10.1016/j.sbi.2008.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 03/18/2008] [Indexed: 11/16/2022]
15
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
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