InterPro in 2019: improving coverage, classification and access to protein sequence annotations

The UniProt Consortium, 2017, UniProt: the universal protein knowledgebase, Nucleic Acids Res., 45, D158, 10.1093/nar/gkw1099

Lewis, 2018, Gene3D: extensive prediction of globular domains in proteins, Nucleic Acids Res., 46, D435, 10.1093/nar/gkx1069

Marchler-Bauer, 2017, CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res., 45, D200, 10.1093/nar/gkw1129

Pedruzzi, 2015, HAMAP in 2015: updates to the protein family classification and annotation system, Nucleic Acids Res., 43, D1064, 10.1093/nar/gku1002

Mi, 2017, PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements, Nucleic Acids Res., 45, D183, 10.1093/nar/gkw1138

Finn, 2016, The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res., 44, D279, 10.1093/nar/gkv1344

Nikolskaya, 2007, PIRSF family classification system for protein functional and evolutionary analysis, Evol. Bioinform. Online, 2, 197

Attwood, 2012, The PRINTS database: a fine-grained protein sequence annotation and analysis resource–its status in 2012, Database (Oxford), 2012, bas019, 10.1093/database/bas019

Bru, 2005, The ProDom database of protein domain families: more emphasis on 3D, Nucleic Acids Res., 33, D212, 10.1093/nar/gki034

Sigrist, 2013, New and continuing developments at PROSITE, Nucleic Acids Res., 41, D344, 10.1093/nar/gks1067

Letunic, 2018, 20 years of the SMART protein domain annotation resource, Nucleic Acids Res., 46, D493, 10.1093/nar/gkx922

Akiva, 2014, The Structure-Function Linkage Database, Nucleic Acids Res., 42, D521, 10.1093/nar/gkt1130

Oates, 2015, The SUPERFAMILY 1.75 database in 2014: a doubling of data, Nucleic Acids Res., 43, D227, 10.1093/nar/gku1041

Haft, 2013, TIGRFAMs and genome properties in 2013, Nucleic Acids Res., 41, D387, 10.1093/nar/gks1234

Piovesan, 2018, MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins, Nucleic Acids Res., 46, D471, 10.1093/nar/gkx1071

Nielsen, 2017, Predicting secretory proteins with SignalP, Methods Mol. Biol., 1611, 59, 10.1007/978-1-4939-7015-5_6

Käll, 2007, Advantages of combined transmembrane topology and signal peptide prediction–the Phobius web server, Nucleic Acids Res., 35, W429, 10.1093/nar/gkm256

Krogh, 2001, Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J. Mol. Biol., 305, 567, 10.1006/jmbi.2000.4315

Lupas, 1991, Predicting coiled coils from protein sequences, Science, 252, 1162, 10.1126/science.252.5009.1162

Durinx, 2017, Identifying ELIXIR Core Data Resources. [version 2; referees: 2 approved], F1000Res, 5, 2422, 10.12688/f1000research.9656.2

Aken, 2016, The Ensembl gene annotation system, Database (Oxford), 2016, baw093, 10.1093/database/baw093

Kersey, 2016, Ensembl Genomes 2016: more genomes, more complexity, Nucleic Acids Res., 44, D574, 10.1093/nar/gkv1209

Mir, 2018, PDBe: towards reusable data delivery infrastructure at protein data bank in Europe, Nucleic Acids Res., 46, D486, 10.1093/nar/gkx1070

Conesa, 2008, Blast2GO: a comprehensive suite for functional analysis in plant genomics, Int. J. Plant Genomics, 2008, 619832, 10.1155/2008/619832

Pedro, 2016, PhytoPath: an integrative resource for plant pathogen genomics, Nucleic Acids Res., 44, D688, 10.1093/nar/gkv1052

Huson, 2016, MEGAN Community edition - interactive exploration and analysis of Large-Scale microbiome sequencing data, PLoS Comput. Biol., 12, e1004957, 10.1371/journal.pcbi.1004957

Mitchell, 2018, EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies, Nucleic Acids Res., 46, D726, 10.1093/nar/gkx967

Jones, 2014, InterProScan 5: genome-scale protein function classification, Bioinformatics, 30, 1236, 10.1093/bioinformatics/btu031

Ashburner, 2000, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat. Genet., 25, 25, 10.1038/75556

Sangrador-Vegas, 2016, GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations, Database (Oxford), 2016, baw027, 10.1093/database/baw027

Finn, 2017, InterPro in 2017-beyond protein family and domain annotations, Nucleic Acids Res., 45, D190, 10.1093/nar/gkw1107

Velankar, 2013, SIFTS: Structure Integration with Function, Taxonomy and Sequences resource, Nucleic Acids Res., 41, D483, 10.1093/nar/gks1258

Watkins, 2017, ProtVista: visualization of protein sequence annotations, Bioinformatics, 33, 2040, 10.1093/bioinformatics/btx120

Pravda, 2018, MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update), Nucleic Acids Res., 46, W368, 10.1093/nar/gky309

Potter, 2018, HMMER web server: 2018 update, Nucleic Acids Res., 46, W200, 10.1093/nar/gky448

Cesare, 2012, Software Similarity and Classification, 10.1007/978-1-4471-2909-7

Das, 2013, Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues, Proc. Natl. Acad. Sci. U.S.A., 110, 13392, 10.1073/pnas.1304749110

Holehouse, 2017, CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins, Biophys. J., 112, 16, 10.1016/j.bpj.2016.11.3200

Das, 2015, Relating sequence encoded information to form and function of intrinsically disordered proteins, Curr. Opin. Struct. Biol., 32, 102, 10.1016/j.sbi.2015.03.008

Necci, 2016, Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe, Protein Sci., 25, 2164, 10.1002/pro.3041