ArticleBMC genomics2009
A proposed syntax for Minimotif Semantics, version 1.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The carboxy-terminus, a key regulator of protein function.Critical reviews in biochemistry and molecular biology · 2019Review
- Minimotif Miner 4: a million peptide minimotifs and counting.Nucleic acids research · 2018Article
- The Functional Human C-Terminome.PloS one · 2016Article
- The minimotif synthesis hypothesis for the origin of life.Journal of translational science · 2016Article
- Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution.Nucleic acids research · 2015Article
- Achieving high accuracy prediction of minimotifs.PloS one · 2012Article
- Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.Nucleic acids research · 2012Article
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- Extremely variable conservation of γ-type small, acid-soluble proteins from spores of some species in the bacterial order Bacillales.Journal of bacteriology · 2011Article
- A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions.Proteins · 2011Article
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- MimoSA: a system for minimotif annotation.BMC bioinformatics · 2010Article
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6 authors.
Funding
Abstract
backgroundOne of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.
resultsHerein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established minimotif sequence definitions was implemented using a relational database management system (RDBMS). To assess the usefulness of our standardized semantics, a series of database queries and stored procedures were used to classify SH3 domain binding minimotifs into 10 groups spanning 700 unique binding sequences.
conclusionOur derived minimotif syntax is currently being used to normalize minimotif covalent chemistry and functional definitions within the MnM database. Analysis of SH3 binding minimotif data spanning many different studies within our database reveals unique attributes and frequencies which can be used to classify different types of binding minimotifs. Implementation of the syntax in the relational database enables the application of many different analysis protocols of minimotif data and is an important tool that will help to better understand specificity of minimotif-driven molecular interactions with proteins.
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