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For: Le Q, Sievers F, Higgins DG. Protein multiple sequence alignment benchmarking through secondary structure prediction. Bioinformatics 2018;33:1331-1337. [PMID: 28093407 PMCID: PMC5408826 DOI: 10.1093/bioinformatics/btw840] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/10/2017] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
1
Kister AE. Beta Sandwich-Like Folds: Sequences, Contacts, Classification of Invariant Substructures and Beta Sandwich Protein Grammar. Methods Mol Biol 2025;2870:51-62. [PMID: 39543030 DOI: 10.1007/978-1-0716-4213-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
2
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]
3
Woźniak T, Sajek M, Jaruzelska J, Sajek MP. RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix. BMC Bioinformatics 2021;22:504. [PMID: 34656080 PMCID: PMC8520625 DOI: 10.1186/s12859-021-04426-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 10/05/2021] [Indexed: 11/15/2022]  Open
4
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 2020;20:1160-1166. [PMID: 28968734 PMCID: PMC6781576 DOI: 10.1093/bib/bbx108] [Citation(s) in RCA: 4436] [Impact Index Per Article: 887.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/27/2017] [Indexed: 11/28/2022]  Open
5
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
6
MacGowan SA, Madeira F, Britto‐Borges T, Warowny M, Drozdetskiy A, Procter JB, Barton GJ. The Dundee Resource for Sequence Analysis and Structure Prediction. Protein Sci 2020;29:277-297. [PMID: 31710725 PMCID: PMC6933851 DOI: 10.1002/pro.3783] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 11/06/2022]
7
Modi V, Dunbrack RL. A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains. Sci Rep 2019;9:19790. [PMID: 31875044 PMCID: PMC6930252 DOI: 10.1038/s41598-019-56499-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/14/2019] [Indexed: 12/21/2022]  Open
8
Structural Characterization of a Unique Peptide in Porin: An Approach Towards Specific Detection of Salmonella enterica Serovar Typhi. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
9
Collins K, Warnow T. PASTA for proteins. Bioinformatics 2019;34:3939-3941. [PMID: 29931282 PMCID: PMC6223367 DOI: 10.1093/bioinformatics/bty495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022]  Open
10
Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2019;34:2490-2492. [PMID: 29506019 PMCID: PMC6041967 DOI: 10.1093/bioinformatics/bty121] [Citation(s) in RCA: 612] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/28/2018] [Indexed: 12/03/2022]  Open
11
Viborg AH, Terrapon N, Lombard V, Michel G, Czjzek M, Henrissat B, Brumer H. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J Biol Chem 2019;294:15973-15986. [PMID: 31501245 PMCID: PMC6827312 DOI: 10.1074/jbc.ra119.010619] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/05/2019] [Indexed: 12/12/2022]  Open
12
Nute M, Saleh E, Warnow T. Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets. Syst Biol 2019;68:396-411. [PMID: 30329135 PMCID: PMC6472439 DOI: 10.1093/sysbio/syy068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 01/15/2023]  Open
13
Emdadi A, Ahmadi Moughari F, Yassaee Meybodi F, Eslahchi C. A novel algorithm for parameter estimation of Hidden Markov Model inspired by Ant Colony Optimization. Heliyon 2019;5:e01299. [PMID: 30923763 PMCID: PMC6422281 DOI: 10.1016/j.heliyon.2019.e01299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/27/2018] [Accepted: 02/27/2019] [Indexed: 11/26/2022]  Open
14
Straub K, Linde M, Kropp C, Blanquart S, Babinger P, Merkl R. Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. Biol Chem 2019;400:367-381. [PMID: 30763032 DOI: 10.1515/hsz-2018-0344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/07/2018] [Indexed: 11/15/2022]
15
Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018;9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022]  Open
16
Disease Sequences High-Accuracy Alignment Based on the Precision Medicine. BIOMED RESEARCH INTERNATIONAL 2018;2018:1718046. [PMID: 29682519 PMCID: PMC5842723 DOI: 10.1155/2018/1718046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/18/2018] [Indexed: 11/18/2022]
17
Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 2017;27:135-145. [PMID: 28884485 DOI: 10.1002/pro.3290] [Citation(s) in RCA: 1207] [Impact Index Per Article: 150.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 01/05/2023]
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