Gene3D: modelling protein structure, function and evolution

Keywords

Chemistry

References

• MUSCLE: a multiple sequence alignment method with reduced time and space complexityR. C. Edgar — 2004
• Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resourceMidori A. Harris — 2004
• Identification and distribution of protein families in 120 completed genomes using Gene3DDavid Lee, Alastair Grant, Russell L. Marsden — 2005
• Evolution of protein superfamilies and bacterial genome size.Juan A. G. Ranea, Daniel Buchan, Janet M. Thornton — 2004
• Assessing strategies for improved superfamily recognitionIan Sillitoe, Mark Dibley, James E. Bray — 2005
• BioMap: gene family based integration of heterogeneous biological databases using AutoMed metadataMichael Maibaum, Galia Rimon, Christine Orengo — 2004
• Basic Charge Clusters and Predictions of Membrane Protein TopologyDavor Juretić, Larisa Zoranić, Damir Zucić — 2002
• MINT: the Molecular INTeraction databaseAndrew Chatr‐aryamontri, Arnaud Céol, Luisa Montecchi Palazzi — 2006
• The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysisFrances M. G. Pearl — 2004
• Integr8 and Genome Reviews: integrated views of complete genomes and proteomesPaul Kersey — 2004
• An efficient algorithm for large-scale detection of protein families.Anton J. Enright — 2002
• SCOP database in 2004: refinements integrate structure and sequence family dataAntonina Andreeva — 2004
• Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.Diana Ekman, Åsa K. Björklund, Johannes Frey-Skött — 2005
• SMART 4.0: towards genomic data integrationIvica Letunić — 2004
• The KEGG resource for deciphering the genomeM. Kanehisa — 2004
• CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteinsEvgenia V. Kriventseva — 2001
• The SUPERFAMILY database in 2004: additions and improvementsMartin Madera — 2004
• The Biomolecular Interaction Network Database and related tools 2005 updateCris Alfarano — 2004
• The COG database: an updated version includes eukaryotesRoman L. Tatusov, Natalie D. Fedorova, John D. Jackson — 2003
• The Distributed Annotation SystemRobin D. Dowell, Rodney M. Jokerst, Allen Day — 2001

Cited by

• Protein domain prediction.Helgi I. Ingólfsson, Golan Yona — 2008
• Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering PlantsEnrique Soler Vázquez — 2015
• A pattern mining approach toward discovering generalized sequence signaturesDietmar H. Dorr, Anne Denton — 2008
• Automated structural annotation of the malaria proteome and identification of candidate proteins for modelling and crystallization studiesYolandi Joubert — 2008
• Étude des mécanismes impliqués dans la tolérance à l'allogreffe cardiaque chez le ratLaëtitia Le Texier — 2012
• Prediction and integration of regulatory and protein-protein interactions.Duangdao Wichadakul, Jason McDermott, Ram Samudrala — 2009
• Target selection for structural genomics: an overview.Russell L. Marsden, Christine Orengo — 2008
• Index-based algorithms for motif search and their integration in a system for differential genome analysisMichael Beckstette — 2007
• Viral Proteins Acquired from a Host Converge to Simplified Domain ArchitecturesNadav Rappoport, Michal Linial — 2012
• Local Function Conservation in Sequence and Structure SpaceNils Weinhold, Oliver Sander, Francisco S. Domingues — 2008
• Towards fully automated structure-based function prediction in structural genomics: a case study.James D. Watson, Steve Sanderson, A. Ezersky — 2007
• Annotating the human proteome: beyond establishing a parts list.Michael Mueller, Lennart Martens, Rolf Apweiler — 2007
• Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer.Sarah Addou, Robert Rentzsch, David Lee — 2009
• LIMLE, a New Molecule Over-Expressed following Activation, Is Involved in the Stimulatory Properties of Dendritic CellsLaëtitia Le Texier, Justine Durand, Amélie Lavault — 2014
• The CATH databaseMichael Knudsen, Carsten Wiuf — 2010
• Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic GenomesJuan A. G. Ranea, Corin Yeats, Alastair Grant — 2007
• Sequence Similarity Network Reveals Common Ancestry of Multidomain ProteinsNan Song, Jacob M. Joseph, George B. Davis — 2008
• In Silico Characterization of Proteins: UniProt, InterPro and Integr8Nicola Mulder, Paul Kersey, Manuela Pruess — 2008
• Data Pushing: A Fly-Centric Guide to Bioinformatics ToolsJames C. Costello, Amy Cash, Mehmet Dalkılıç — 2008
• Domain Architecture Comparison for Multidomain Homology IdentificationNan Song, R. D. Sedgewick, Dannie Durand — 2007

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