A unique approach for protein secondary structure comparison under TOPS representation

References

• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Cao, C., Wang, G., Liu, A., Xu, S., Wang, L., & Zou, S. (2016). A new secondary structure assignment algorithm using cα backbone fragments. International Journal of Molecular Sciences, 17(3), 333. https://doi.org/10.3390/ijms17030333
   PubMed Web of Science ®Google Scholar
• Cao, C., & Xu, S. (2016). Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area. Scientific Reports, 6(1), 33232. https://doi.org/10.1038/srep33232
   PubMedGoogle Scholar
• Cao, C., Xu, S., & Wang, L. (2015). An algorithm for protein helix assignment using helix geometry. PLoS One, 10(7), e0129674. https://doi.org/10.1371/journal.pone.0129674
   PubMed Web of Science ®Google Scholar
• Chew, L. P., & Kedem, K. (2002, June). Finding the consensus shape for a protein family. In Proceedings of the Eighteenth Annual Symposium on Computational Geometry (pp. 64–73). https://doi.org/10.1145/513400.513408
   Google Scholar
• Das, S., Deb, T., Dey, N., Ashour, A. S., Bhattacharya, D. K., & Tibarewala, D. N. (2018). Optimal choice of k-mer in composition vector method for genome sequence comparison. Genomics, 110(5), 263–273. https://doi.org/10.1016/j.ygeno.2017.11.003
   PubMed Web of Science ®Google Scholar
• Dey, S., Ghosh, P., & Das, S. (2023). Positional difference and frequency (PdF) based alignment-free technique for genome sequence comparison. Journal of Biomolecular Structure & Dynamics, 1–29. https://doi.org/10.1080/07391102.2023.2272748
   Web of Science ®Google Scholar
• Eidhammer, I., Jonassen, I., & Taylor, W. R. (2004). Protein Bioinformatics: An algorithmic approach to sequence and structure analysis (Vol. 1). Wiley.
   Google Scholar
• Gabanyi, M. J., Adams, P. D., Arnold, K., Bordoli, L., Carter, L. G., Flippen-Andersen, J., Gifford, L., Haas, J., Kouranov, A., McLaughlin, W. A., Micallef, D. I., Minor, W., Shah, R., Schwede, T., Tao, Y.-P., Westbrook, J. D., Zimmerman, M., & Berman, H. M. (2011). The structural biology knowledgebase: A portal to protein structures, sequences, functions, and methods. Journal of Structural and Functional Genomics, 12(2), 45–54. https://doi.org/10.1007/s10969-011-9106-2
   PubMedGoogle Scholar
• Ghosh, S., Pal, J., Cattani, C., Maji, B., & Bhattacharya, D. K. (2023). Protein sequence comparison based on representation on a finite dimensional unit hypercube. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/10.1080/07391102.2023.2268719
   Web of Science ®Google Scholar
• Gilbert, D., Rosselló, F., Valiente, G., & Veeramalai, M. (2006). Alignment-free comparison of tops strings. London Algorithmics and Stringology, 8, 177–197.
   Google Scholar
• Gilbert, D., Westhead, D., Nagano, N., & Thornton, J. (1999). Motif-based searching in TOPS protein topology databases. Bioinformatics (Oxford, England), 15(4), 317–326. https://doi.org/10.1093/bioinformatics/15.4.317
   PubMed Web of Science ®Google Scholar
• Grabowski, M., Niedzialkowska, E., Zimmerman, M. D., & Minor, W. (2016). The impact of structural genomics: The first quindecennial. Journal of Structural and Functional Genomics, 17(1), 1–16. https://doi.org/10.1007/s10969-016-9201-5
   PubMedGoogle Scholar
• Guo, Y., & Wang, T. M. (2008). A new method to analyze the similarity of protein structure using TOPS representations. Journal of Biomolecular Structure & Dynamics, 26(3), 367–374. https://doi.org/10.1080/07391102.2008.10507251
   PubMed Web of Science ®Google Scholar
• Kufareva, I., & Abagyan, R. (2012). Methods of protein structure comparison. In A. J. W. Orry (Ed.), Homology Modelling: Methods and Protocols (pp. 231–257). New York: Humana Press.
   Google Scholar
• Li, B., Li, Y. B., & He, H. B. (2005). LZ complexity distance of DNA sequences and its application in phylogenetic tree reconstruction. Genomics, Proteomics & Bioinformatics, 3(4), 206–212. https://doi.org/10.1016/s1672-0229(05)03028-7
   PubMedGoogle Scholar
• Liu, L., & Wang, T. (2008). Comparison of TOPS strings based on LZ complexity. Journal of Theoretical Biology, 251(1), 159–166. https://doi.org/10.1016/j.jtbi.2007.11.016
   PubMed Web of Science ®Google Scholar
• Mat-Sharani, S., Quay, D. H., Ng, C. L., & Raih, M. F. (2019). Structural genomics. Universiti Kebangsaan Malaysia, Selangor, Malaysia. Encyclopedia of Bioinformatics and Computational Biology, 3, 722–728. https://doi.org/10.1016/B978-0-12-809633-8.20155-6
   Google Scholar
• Michalopoulos, I., Torrance, G. M., Gilbert, D. R., & Westhead, D. R. (2004). TOPS: An enhanced database of protein structural topology. Nucleic Acids Research, 32(Database issue), D251–D254. https://doi.org/10.1093/nar/gkh060
   PubMedGoogle Scholar
• Riley, A. C., Ashlock, D. A., & Graether, S. P. (2023). The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny. PLoS One, 18(7), e0288388. https://doi.org/10.1371/journal.pone.0288388
   PubMed Web of Science ®Google Scholar
• Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
   PubMed Web of Science ®Google Scholar
• Terwilliger, T. C., Stuart, D., & Yokoyama, S. (2009). Lessons from structural genomics. Annual Review of Biophysics, 38(1), 371–383. https://doi.org/10.1146/annurev.biophys.050708.133740
   PubMedGoogle Scholar
• Veeramalai, M., Gilbert, D., & Valiente, G. (2010). An optimized TOPS + comparison method for enhanced TOPS models. BMC Bioinformatics, 11(1), 138. https://doi.org/10.1186/1471-2105-11-138
   PubMedGoogle Scholar
• Wen, J., & Li, C. (2007). Similarity analysis of DNA sequences based on the LZ complexity. Internet Electronic Journal of Molecular Design, 6, 1–12.
   Google Scholar
• Wu, R., Ding, F., Wang, R., Shen, R., Zhang, X., Luo, S., Su, C., Wu, Z., Xie, Q., Berger, B., Ma, J., & Peng, J. (2022). High-resolution de novo structure prediction from primary sequence. BioRxiv, 2022–07.
   Google Scholar