ProFAT: a web-based tool for the functional annotation of protein sequences

Keywords

Annotation, Computer science, Biological database, Protein structure database, Context (archaeology)

References

• Overexpression of poly(A) binding protein prevents maturation‐specific deadenylation and translational inactivation in Xenopus oocytes.Michael Wormington, Anjanette M. Searfoss, Carol A. Hurney — 1996
• Analysis of compositionally biased regions in sequence databases.John C. Wootton, Scott Federhen — 1996
• Eps8 in the midst of GTPases.Pier Paolo Di Fiore, Giorgio Scita — 2002
• Interaction of eIF4G with poly(A)-binding protein stimulates translation and is critical for Xenopus oocyte maturation.Motoaki Wakiyama, Hiroaki Imataka, Nahum Sonenberg — 2000
• Eco1 is a novel acetyltransferase that can acetylate proteins involved in cohesion.Dmitri Ivanov, Alexander Schleiffer, Frank Eisenhaber — 2002
• APPL proteins link Rab5 to nuclear signal transduction via an endosomal compartment.Marta Miączyńska, Savvas Christoforidis, Angelika Giner — 2004
• Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La proteinCaterina Alfano, Domenico Sanfelice, Jeffrey J. Babon — 2004
• Cloning and characterization of KPL2, a novel gene induced during ciliogenesis of tracheal epithelial cells.Lawrence E. Ostrowski, Kaya L. Andrews, Pravin D. Potdar — 1999
• CD-Search: protein domain annotations on the flyAron Marchler‐Bauer, Stephen H. Bryant — 2004
• Poly(A) Tail Shortening by a Mammalian Poly(A)-specific 3′-Exoribonuclease*Christof G. Körner, Elmar Wahle — 1997
• Protein structure comparison by alignment of distance matrices.Liisa Holm, Chris Sander — 1993
• Predicting coiled coils from protein sequencesAndrei N. Lupas, Marc Van Dyke, Jeff Stock — 1991
• A new approach to protein fold recognitionD. T. Jones, W. R. Taylort, Janet M. Thornton — 1992
• Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structureDavid T. Jones, Michael L. Tress, Kevin Bryson — 1999
• Cpc1, a Chlamydomonas central pair protein with an adenylate kinase domainHui Zhang, David R. Mitchell — 2004
• OntoBlast function: from sequence similarities directly to potential functional annotations by ontology termsG. Zehetner — 2003
• An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig.Anu Sironen, Bo Thomsen, Magnus Andersson — 2006
• RNA-binding proteins in mouse oocytes and embryos: expression of genes encoding Y box, DEAD box RNA helicase, and polyA binding proteins.Barbara V. Paynton — 1998
• Multiple sequence alignment with the Clustal series of programsR. Chenna — 2003
• An algorithm for suffix strippingMartin Porter — 1997

Cited by

• HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold RecognitionP.H. Given, J.R. Jones — 2011
• Machine Learning Approaches to BioinformaticsZheng Rong Yang — 2010
• Lost in the space of bioinformatic tools: a constantly updated survival guide for genetic epidemiology. The GenEpi Toolbox.Stefan Coassin, Anita Kloss‐Brandstätter, Florian Kronenberg — 2010
• Improving classification in protein structure databases using text miningAntonis Koussounadis, Oliver Redfern, David T. Jones — 2009
• Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52.Axel Erler, Susanne Wegmann, Céline Élie-Caille — 2009
• A transparent collaborative framework for efficient data analysis and knowledge annotation on the webN. Samatova, P. Breimyer — 2009
• An In Silico Approach for Function Prediction of Hypothetical Proteins of Mycobacterium laprae TNHardik Sorathiya, Aishwarya Jadeja, John J. Georrge — 2020
• Cold-Induced Reprogramming of Subcutaneous White Adipose Tissue Assessed by Single-Cell and Single-Nucleus RNA SequencingQing Liu, Qiaoyun Long, Jiayu Zhao — 2023
• Conformational Adaptability of Red β during DNA Annealing and Implications for Its Structural Relationship with Rad 52A. Erler, Susanne Wegmann, C. Élie-Caille — 2009
• Bioinformatic Tools for the Search of Disease-Associated VariationsS. Coassin, A. Kloss-Brandstätter, F. Kronenberg — 2012

Related papers

• DWARF – a data warehouse system for analyzing protein familiesMarkus Fischer, Quan Ke Thai, Melanie Grieb — 2006
• Functional annotation of proteomic sequences based on consensus of sequence and structural analysisDavid H. Kitson — 2002
• Functional annotation by identification of local surface similarities: a novel tool for structural genomicsFabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni — 2005
• The future of structural bioinformatics in the post-genomic eraDimitriοs Vlachakis, Dimosthenis Tsagkrasoulis, Georgia Tsiliki — 2012
• The SYSTERS Protein Family Database in 2005Thomas R. Meinel — 2004
• Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks.Janine N. Copp, Eyal Akiva, Patricia C. Babbitt — 2018
• Structure-based functional annotation of protein sequences guided by comparative modelsMelissa Standley, Akira R. Kinjo, Mark van der Giezen — 2008