Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

Keywords

Biology, Annotation, Computational biology, Genomics, Functional genomics

References

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• MINT: the Molecular INTeraction databaseAndrew Chatr‐aryamontri, Arnaud Céol, Luisa Montecchi Palazzi — 2006
• The STRING database in 2011: functional interaction networks of proteins, globally integrated and scoredDamian Szklarczyk, Andrea Franceschini, Michael Kuhn — 2010
• Gene3D: merging structure and function for a Thousand genomesJonathan Lees, Corin Yeats, Oliver Redfern — 2009
• DIMA 3.0: Domain Interaction MapQi Luo, Philipp Pagel, Baiba Vilne — 2010
• The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold SpaceAlison Cuff, Oliver Redfern, Lesley H. Greene — 2009
• Maximal chromosome compaction occurs by axial shortening in anaphase and depends on Aurora kinaseFelipe Mora‐Bermúdez, Daniel W. Gerlich, Jan Ellenberg — 2007
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• SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogenyDerek A. Wilson, Ralph Pethica, Yiduo Zhou — 2008
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Cited by

• Data Mining Techniques for the Life SciencesOliviero Carugo, Frank Eisenhaber — 2009
• The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthasesArne Schwelm, Johan Fogelqvist, Andrea Knaust — 2015
• Using CATH‐Gene3D to Analyze the Sequence, Structure, and Function of ProteinsIan Sillitoe, Tony E. Lewis, Christine Orengo — 2015
• Clustering and Classification of Multi-domain ProteinsNeethu Shah — 2013
• Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of ImmunityNidhi Tyagi, Edward Farnell, Colin M. Fitzsimmons — 2015
• Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds.Debmalya Barh, Krishna Kant Gupta, Neha Jain — 2013
• Skipper genome sheds light on unique phenotypic traits and phylogenyQian Cong, Dominika Borek, Zbyszek Otwinowski — 2015
• Protein structure prediction from sequence variationDebora S. Marks, Thomas A. Hopf, Chris Sander — 2012
• A Method for WD40 Repeat Detection and Secondary Structure PredictionYang Wang, Fan Jiang, Zhu Zhuo — 2013
• EC-BLAST: A Tool to Automatically Search and Compare Enzyme ReactionsSyed Asad Rahman, Sergio Martínez Cuesta, Nicholas Furnham — 2014
• PainNetworks: A web-based resource for the visualisation of pain-related genes in the context of their network associationsJames R. Perkins, Jonathan Lees, Ana Antunes‐Martins — 2013
• Large α-aminonitrilase activity screening of nitrilase superfamily members: Access to conversion and enantiospecificity by LC–MSFranck Bordier, Mark Stam, Ekaterina Darii — 2014
• Protein Modelling: What Happened to the “Protein Structure Gap”?Torsten Schwede — 2013
• Gene3D: Multi-domain annotations for protein sequence and comparative genome analysisJonathan Lees, David Lee, Romain A. Studer — 2013
• One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic treesRosanna G. Alderson, Daniel Barker, John B. O. Mitchell — 2014
• EBI metagenomics—a new resource for the analysis and archiving of metagenomic dataSarah Hunter, Matthew J. Corbett, Hubert Denise — 2013
• InterProScan 5: genome-scale protein function classificationPhilip Jones, David Binns, Hsin-Yu Chang — 2014
• New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structuresIan Sillitoe, Alison Cuff, Benoît H. Dessailly — 2012
• Protein function prediction by massive integration of evolutionary analyses and multiple data sourcesDomenico Cozzetto, Daniel Buchan, Kevin Bryson — 2013
• The Structure–Function Linkage DatabaseEyal Akiva, Shoshana Brown, Daniel E. Almonacid — 2013

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