Areal H, Abrantes J, Esteves PJ (2011) Signatures of positive selection in Toll-like receptor (TLR) genes in mammals. BMC Evol Biol 11:368. https://doi.org/10.1186/1471-2148-11-368

Article  CAS  PubMed  PubMed Central  Google Scholar 

Botos I, Segal DM, Davies DR (2011) The structural biology of Toll-like receptors. Structure 19:447–459. https://doi.org/10.1016/j.str.2011.02.004

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cook DN, Pisetsky DS, Schwartz DA (2004) Toll-like receptors in the pathogenesis of human disease. Nat Immunol 5:975–979. https://doi.org/10.1038/ni1116

Article  CAS  PubMed  Google Scholar 

de Castro E, Sigrist CJ, Gattiker A et al (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34(W362):W365. https://doi.org/10.1093/nar/gkl124

Article  CAS  Google Scholar 

Ghosh M, Basak S, Dutta S (2022) Natural selection shaped the evolution of amino acid usage in mammalian toll like receptor genes. Comput Biol Chem 97:107637. https://doi.org/10.1016/j.compbiolchem.2022.107637

Article  CAS  PubMed  Google Scholar 

Gumulya Y, Gillam EM (2017) Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering. Biochem J 474:1–19. https://doi.org/10.1042/BCJ20160507

Article  CAS  PubMed  Google Scholar 

Karapetyan L, Luke JJ, Davar D (2020) Toll-like receptor 9 agonists in cancer. Onco Targets Ther 13:10039–10060. https://doi.org/10.2147/OTT.S247050

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khan RT, Musil M, Stourac J (2021) Fully automated ancestral sequence reconstruction using FireProtASR. Curr Protoc 1:e30. https://doi.org/10.1002/cpz1.30

Article  CAS  PubMed  Google Scholar 

Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096

Article  CAS  PubMed  PubMed Central  Google Scholar 

Madeira F, Pearce M, Tivey ARN et al (2022) Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 50:W276–W279. https://doi.org/10.1093/nar/gkac240

Article  CAS  PubMed  PubMed Central  Google Scholar 

Merkl R, Sterner R (2016) Ancestral protein reconstruction: techniques and applications. Biol Chem 397:1–21. https://doi.org/10.1515/hsz-2015-0158

Article  CAS  PubMed  Google Scholar 

Mirdita M, Schütze K, Moriwaki Y et al (2022) ColabFold: making protein folding accessible to all. Nat Methods 19:679–682. https://doi.org/10.1038/s41592-022-01488-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Muffato M, Louis A, Nguyen NTT (2023) Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom. Nat Ecol Evol 7:355–366. https://doi.org/10.1038/s41559-022-01956-z

Article  PubMed  PubMed Central  Google Scholar 

Musil M, Khan RT, Beier A et al (2021) FireProtASR a web server for fully automated ancestral sequence reconstruction. Brief Bioinform 22:bbaa337. https://doi.org/10.1093/bib/bbaa337

Article  PubMed  Google Scholar 

Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426. https://doi.org/10.1093/oxfordjournals.molbev.a040410

Article  CAS  PubMed  Google Scholar 

Nie L, Cai SY, Shao JZ et al (2018) Toll-like receptors, associated biological roles, and signaling networks in non-mammals. Front Immunol 9:1523. https://doi.org/10.3389/fimmu.2018.01523

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peden JF (2000) Analysis of codon usage (Doctoral dissertation). University of Nottingham, United Kingdom

Google Scholar 

Roach JC, Glusman G, Rowen L et al (2005) The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci USA 102:9577–9582. https://doi.org/10.1073/pnas.0502272102

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Roy A, Banerjee R, Basak S (2017) HIV progression depends on codon and amino acid usage profile of envelope protein and associated host-genetic influence. Front Microbiol 8:1083. https://doi.org/10.3389/fmicb.2017.01083

Article  PubMed  PubMed Central  Google Scholar 

Takeda K, Akira S (2005) Toll-like receptors in innate immunity. Int Immunol 17:1–14. https://doi.org/10.1093/intimm/dxh186

Article  CAS  PubMed  Google Scholar 

Vidya MK, Kumar VG, Sejian V et al (2018) Toll-like receptors: significance, ligands, signaling pathways, and functions in mammals. Int Rev Immunol 37:20–36. https://doi.org/10.1080/08830185.2017.1380200

Article  CAS  PubMed  Google Scholar 

Yan Y, Zhang D, Zhou P et al (2017) HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res 45:W365–W373. https://doi.org/10.1093/nar/gkx407

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591. https://doi.org/10.1093/molbev/msm088

Article  CAS  PubMed  Google Scholar 

Yang Z, Zeng X, Zhao Y et al (2023) AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 8:115. https://doi.org/10.1038/s41392-023-01381-z

Article  PubMed  PubMed Central  Google Scholar 

Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33:2302–2309. https://doi.org/10.1093/nar/gki524

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhou W, Li Y, Pan X, Gao Y et al (2013) Toll-like receptor 9 interaction with CpG ODN–an in silico analysis approach. Theor Biol Med Model 10:18. https://doi.org/10.1186/1742-4682-10-18

Article  CAS  PubMed  PubMed Central  Google Scholar