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For: Sievers F, Higgins DG. QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. Bioinformatics 2019;36:90-95. [PMID: 31292629 PMCID: PMC9881607 DOI: 10.1093/bioinformatics/btz552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/17/2019] [Accepted: 07/09/2019] [Indexed: 02/02/2023]  Open
Number Cited by Other Article(s)
1
Tharanga S, Ünlü ES, Hu Y, Sjaugi MF, Çelik MA, Hekimoğlu H, Miotto O, Öncel MM, Khan AM. DiMA: sequence diversity dynamics analyser for viruses. Brief Bioinform 2024;26:bbae607. [PMID: 39592151 PMCID: PMC11596295 DOI: 10.1093/bib/bbae607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 09/22/2024] [Accepted: 11/13/2024] [Indexed: 11/28/2024]  Open
2
Xu J, Ye S, Guan F. A computational strategy to improve the activity of tyrosine phenol-lyase for the synthesis of L-DOPA. Sci Rep 2024;14:25329. [PMID: 39455666 PMCID: PMC11512013 DOI: 10.1038/s41598-024-76111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Accepted: 10/10/2024] [Indexed: 10/28/2024]  Open
3
Karas M, Vešelényiová D, Boszorádová E, Nemeček P, Gerši Z, Moravčíková J. Comparative Analysis of Dehydrins from Woody Plant Species. Biomolecules 2024;14:250. [PMID: 38540671 PMCID: PMC10967807 DOI: 10.3390/biom14030250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/18/2024] [Indexed: 11/11/2024]  Open
4
McWhite CD, Armour-Garb I, Singh M. Leveraging protein language models for accurate multiple sequence alignments. Genome Res 2023;33:1145-1153. [PMID: 37414576 PMCID: PMC10538487 DOI: 10.1101/gr.277675.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
5
Santus L, Garriga E, Deorowicz S, Gudyś A, Notredame C. Towards the accurate alignment of over a million protein sequences: Current state of the art. Curr Opin Struct Biol 2023;80:102577. [PMID: 37012200 DOI: 10.1016/j.sbi.2023.102577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 04/04/2023]
6
Sharkey RE, Herbert JB, McGaha DA, Nguyen V, Schoeffler AJ, Dunkle JA. Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA. RNA (NEW YORK, N.Y.) 2022;28:210-226. [PMID: 34795028 PMCID: PMC8906542 DOI: 10.1261/rna.078946.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
7
Lichman BR. Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution. Methods Mol Biol 2022;2505:165-179. [PMID: 35732944 DOI: 10.1007/978-1-0716-2349-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
8
Emms DM, Kelly S. Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench. Genome Biol Evol 2020;12:2258-2266. [PMID: 33022036 PMCID: PMC7738749 DOI: 10.1093/gbe/evaa211] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 01/24/2023]  Open
9
Wright ES. RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. RNA (NEW YORK, N.Y.) 2020;26:531-540. [PMID: 32005745 PMCID: PMC7161358 DOI: 10.1261/rna.073015.119] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/28/2020] [Indexed: 05/05/2023]
10
Torrisi M, Pollastri G, Le Q. Deep learning methods in protein structure prediction. Comput Struct Biotechnol J 2020;18:1301-1310. [PMID: 32612753 PMCID: PMC7305407 DOI: 10.1016/j.csbj.2019.12.011] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/01/2023]  Open
11
Lassmann T. Kalign 3: multiple sequence alignment of large data sets. Bioinformatics 2019;36:btz795. [PMID: 31665271 PMCID: PMC7703769 DOI: 10.1093/bioinformatics/btz795] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022]  Open
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