Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517595 | PMC |
| http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049957 | PLOS |
Publication Analysis
Top Keywords
Similar Publications
Secondary structure, a missing component of sequence-based minimotif definitions.
PLoS One
May 2013
School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.
Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs.
View Article and Find Full Text PDFA proposed syntax for Minimotif Semantics, version 1.
BMC Genomics
August 2009
Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030-3305 USA.
Background: One 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.
View Article and Find Full Text PDFMinimotif miner 2nd release: a database and web system for motif search.
Nucleic Acids Res
January 2009
Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06029-2155, USA.
Article Synopsis
- Minimotif Miner (MnM) is a tool that helps predict the functions of protein motifs by comparing user-provided protein queries to a vast database of motifs, now expanded to about 5000.
- The latest version of MnM features a revamped web application with enhancements like better navigation, video tutorials, support for alternative names, and more in-depth SNP analysis.
- A practical example of MnM's capabilities is demonstrated with an analysis of prion proteins, highlighting the tool's utility for researchers.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!