References
Literature
1) PyHMMER (Larralde et al., 2022), a Python library binding to HMMER (Eddy, 2011).
2) Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics.
3) Korendovych, Ivan V., and William F. DeGrado. “De Novo Protein Design, a Retrospective.” Quarterly Reviews of Biophysics 53 (2020): e3. https://doi.org/10.1017/S0033583519000131.
4) Sonnhammer, Erik L.L., Sean R. Eddy, and Richard Durbin. “Pfam: A Comprehensive Database of Protein Domain Families Based on Seed Alignments.” Proteins: Structure, Function, and Genetics 28, no. 3 (July 1997): 405–20. https://doi.org/10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L.
5) Gromiha, M. Michael, Raju Nagarajan, and Samuel Selvaraj. “Protein Structural Bioinformatics: An Overview.” In Encyclopedia of Bioinformatics and Computational Biology, 445–59. Elsevier, 2019. https://doi.org/10.1016/B978-0-12-809633-8.20278-1.
6) Baker, David, and Andrej Sali. “Protein Structure Prediction and Structural Genomics.” Science 294, no. 5540 (October 5, 2001): 93–96. https://doi.org/10.1126/science.1065659.
7) Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B. Gasser, Zuoren Yang*, Lukasz Kurgan*, Jiangning Song*, iFeatureOmega – an integrative platform for the feature engineering, visualization and analysis of features from molecular sequence, structural and ligand data sets. Nucleic Acids Research , 2022.
8) Pearson, William R. “An Introduction to Sequence Similarity (‘Homology’) Searching.” Current Protocols in Bioinformatics 42, no. 1 (June 2013). https://doi.org/10.1002/0471250953.bi0301s42.
9) Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova and Adam Godzik. “FATCAT 2.0: towards a better understanding of the structural diversity of proteins” Nucleic Acids Res., May 2020. gkaa443, https://doi.org/10.1093/nar/gkaa443
Python Packages