Minimotif Miner: a tool for investigating protein function

@article{Balla2006MinimotifMA,
  title={Minimotif Miner: a tool for investigating protein function},
  author={Sudha Balla and Vishal Thapar and Snigdha Verma and T. Y. Luong and Tanaz Faghri and Chun-Hsi Huang and Sanguthevar Rajasekaran and Jacob J. del Campo and Jessica H Shinn and William Mohler and Mark W. Maciejewski and Michael Robert Gryk and Bryan Piccirillo and Stanley R Schiller and Martin R. Schiller},
  journal={Nature Methods},
  year={2006},
  volume={3},
  pages={175-177}
}
In addition to large domains, many short motifs mediate functional post-translational modification of proteins as well as protein-protein interactions and protein trafficking functions. We have constructed a motif database comprising 312 unique motifs and a web-based tool for identifying motifs in proteins. Functional motifs predicted by MnM can be ranked by several approaches, and we validated these scores by analyzing thousands of confirmed examples and by confirming prediction of previously… 

Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity

  • M. Schiller
  • Biology, Computer Science
    Current protocols in protein science
  • 2007
TLDR
Scoring based on evolutionary conservation, protein surface prediction, and motif frequency can be used in conjunction with other motif programs and the known biology of the query to reduce false‐positive predictions and select short motifs for experimental pursuit.

Computational Techniques for Motif Search

TLDR
This paper survey some of the techniques that have been proposed in the literature for motifs identification in the study of protein-protein interactions and finds that they are typically very short.

Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset

TLDR
This investigation demonstrates the important effects of a high-quality negative dataset on the performance of such statistical inference and proposes an approach to discovering motif pairs at interaction sites that are essential for understanding protein functions and helpful for the rational design of protein engineering and folding experiments.

Structural conservation of a short, functional, peptide-sequence motif.

TLDR
The many bioinformatic tools and resources which discover, define and catalogue the various, known protein domains as well as assist users by identifying domain signatures within proteins of interest are reviewed.

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

TLDR
It is shown that short, linear protein motifs can be efficiently recovered from proteome-scale datasets such as sub-cellular localization, molecular function, half-life, and protein abundance data using an information theoretic approach and these predicted motifs provide focused hypotheses for experimental validation.

In silico protein motif discovery and structural analysis.

TLDR
This chapter collects some of the most common and useful tools available for protein motif discovery and secondary and tertiary structure prediction from a primary amino acid sequence and provides pointers to many other tools.

A computational strategy for the prediction of functional linear peptide motifs in proteins

TLDR
This procedure for the identification of functional motifs, which scores pattern conservation in homologous sequences by taking explicitly into account the sequence similarity to the query sequence, is developed and helpful to guide experiments because it allows focusing on those short linear peptide motifs that have a high probability to be functional.

Computational identification and analysis of protein short linear motifs.

TLDR
Focusing on disordered regions of proteins, where SLiMs are predominantly found, and masking out non-conserved residues can reduce the level of noise but more work is required to improve the quality of high-throughput experimental datasets as input for computational discovery.

A new protein linear motif benchmark for multiple sequence alignment software

TLDR
None of the programs currently available is capable of reliably aligning LMs in distantly related sequences and a number of specific problems are highlighted.

Discovering Interaction Motifs from Protein Interaction Networks

TLDR
This chapter provides a review on the different approaches on finding interaction motifs with a discussion on their implications, potentials and possible areas of improvements in the future.
...

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