3.1 - ACKNOWLEDGEMENTS
This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642095 for the OPATHY consortium, by the pre-doctoral research fellowship from Industrial Doctorates of MINECO (Grant 659 DI-17-09134); by the State Plan for Scientific and Technical Research and Innovation 2017-2020 under the Grant TSI-100903-2019-11 from the Secretary of State for Digital Advancement from Ministry of Economic Affairs and Digital Transformation, Spain; and by Expedient IDI-2021-158274-a from Ministry of Science and Innovation, Spain
3.2 - LITERATURE CITED
- Akiva E, Brown S, Almonacid DE, et al. 2014. The Structure-Function Linkage Database. Nucleic Acids Res 42: D521-530. doi: 10.1093/nar/gkt1130
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
- Attwood TK, Beck ME, Bleasby AJ and Parry-Smith DJ. 1994. PRINTS--a database of protein motif fingerprints. Nucleic Acids Res 22: 3590-3596.
- Bairoch A. 2000. The ENZYME database in 2000. Nucleic Acids Res 28: 304-305.
- Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2013. GenBank. Nucleic Acids Res. 41(Database issue):D36-42. doi: 10.1093/nar/gks1195.
- Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M and Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
- Coordinators NR. 2017. Database Resources of the National Center for Biotechnology Information. Nucleic Acids Res 45: D12-D17. doi: 10.1093/nar/gkw1071
- Corpet F, Servant F, Gouzy J and Kahn D. 2000. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 28: 267-269.
- Cunningham F, Amode MR, Barrell D, et al. 2015. Ensembl 2015. Nucleic Acids Res 43: D662-669. doi: 10.1093/nar/gku1010
- Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I. 2017. CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res. 45(D1)
- Finn RD, Attwood TK, Babbitt PC, et al. 2017. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45: D190-D199. doi: 10.1093/nar/gkw1107
- Finn RD, Coggill P, Eberhardt RY, et al. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44: D279-285. doi: 10.1093/nar/gkv1344
- Fleischmann A, Darsow M, Degtyarenko K, et al. 2004. IntEnz, the integrated relational enzyme database. Nucleic Acids Res 32: D434-437. doi: 10.1093/nar/gkh119
- Gough, J., Karplus, K., Hughey, R. and Chothia, C. 2001."Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. J. Mol. Biol., 313(4), 903-919.
- Haft DH, Selengut JD and White O. 2003. The TIGRFAMs database of protein families. Nucleic Acids Res 31: 371-373.
- Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ and O'Donovan C. 2015. The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res 43: D1057-1063. doi: 10.1093/nar/gku1113
- Jones P, Binns D, Chang HY, et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30: 1236-1240. doi: 10.1093/bioinformatics/btu031
- Kotera M, Hirakawa M, Tokimatsu T, Goto S and Kanehisa M. 2012. The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods MolBiol 802: 19-39.
- Letunic I and Bork P. 2018. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res 46: D493-D496. doi: 10.1093/nar/gkx922
- Marchler-Bauer A, Lu S, Anderson JB, et al. 2011. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-D229.
- Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D and Thomas PD. 2017. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res 45: D183-D189. doi: 10.1093/nar/gkw1138
- Nikolskaya AN, Arighi CN, Huang H, Barker WC and Wu CH. 2007. PIRSF family classification system for protein functional and evolutionary analysis. Evolutionary bioinformatics online 2: 197-209.
- Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S. 2015. HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Research, Volume 43, Issue D1, 28 Pages D1064–D1070
- Piovesan D, Tabaro F, Paladin L, et al. 2018. MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res 46: D471-D476. doi: 10.1093/nar/gkx1071
- M, Lane L, Boutet E, Lieberherr D, Tognolli M, Bougueleret L and Bairoch A. 2009. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. Journal of proteomics 72: 567-573. doi: 10.1016/j.jprot.2008.11.010
- Sigrist CJA, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I. 2012. New and continuing developments at PROSITE. Nucleic Acids Res. doi: 10.1093/nar/gks1067
- Yates B, Braschi B, Gray K, Seal R, Tweedie S, Bruford E. 2017. Genenames.org: the HGNC and VGNC resources in 2017. 2017. Nucleic Acids Res. 45(D1):D619-625.
