Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
TLDR
The results show that traditional scores for sequence and structure similarity have the same basic exponential relationship as observed previously, with structural divergence, measured in RMS, being exponentially related to sequence divergence, Measurements have greater statistical weight and precision.About:
This article is published in Journal of Molecular Biology.The article was published on 2000-03-17 and is currently open access. It has received 395 citations till now. The article focuses on the topics: Similarity (network science).read more
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The COG database: an updated version includes eukaryotes
Roman L. Tatusov,Natalie D. Fedorova,John D. Jackson,Aviva R. Jacobs,Boris Kiryutin,Eugene V. Koonin,Dmitri M. Krylov,Raja Mazumder,Sergei L. Mekhedov,Anastasia N. Nikolskaya,B Sridhar Rao,Sergei Smirnov,Alexander V. Sverdlov,Sona Vasudevan,Yuri I. Wolf,Jodie J. Yin,Darren A. Natale +16 more
TL;DR: A major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes is described and is expected to be a useful platform for functional annotation of newlysequenced genomes, including those of complex eukARYotes, and genome-wide evolutionary studies.
Journal ArticleDOI
The Calpain System
TL;DR: How calpain activity is regulated in cells is still unclear, but the calpains ostensibly participate in a variety of cellular processes including remodeling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis.
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A census of human transcription factors: function, expression and evolution
Juan M. Vaquerizas,Sarah K. Kummerfeld,Sarah K. Kummerfeld,Sarah A. Teichmann,Nicholas M. Luscombe,Nicholas M. Luscombe +5 more
TL;DR: An analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and evolutionary conservation provides a solid foundation for future investigations to elucidate regulatory mechanisms underlying diverse mammalian biological processes.
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Prediction of protein function from protein sequence and structure.
TL;DR: The state of the art in function prediction is reviewed and some of the underlying difficulties and successes are described, including inferring conservation patterns in members of a functionally uncharacterized family for which many sequences and structures are known.
Journal ArticleDOI
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
Andreas Ruepp,Alfred Zollner,Dieter Maier,Kaj Albermann,Jean Hani,Martin Mokrejs,Igor V. Tetko,Ulrich Güldener,Gertrud Mannhaupt,Martin Münsterkötter,H. Werner Mewes +10 more
TL;DR: The Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism, is presented.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
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