Related Experiment Video
Updated: Dec 26, 2025
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
10.7K
Leitmotif: protein motif scanning 2.0
Siniša Biđin1, Ivan Vujaklija1, Tina Paradžik2
1Faculty of Electrical Engineering and Computing, University of Zagreb, 10 000 Zagreb, Croatia.
Bioinformatics (Oxford, England)
|March 11, 2020
Summary
Leitmotif is a new web application for Motif-HMM (mHMM) scanning, offering advantages over standard methods for protein motif analysis. This tool enhances protein discrimination, particularly for variations within conserved motifs or potential false positives.
Area of Science:
- Bioinformatics
- Computational Biology
- Protein Sequence Analysis
Background:
- Standard sequence-profile search methods like HMMER and PSI-BLAST have limitations in discriminating proteins with variations in conserved motifs.
- Motif-HMM (mHMM) scanning offers unique advantages for identifying protein family subtypes and filtering false positives, such as pseudoenzymes.
Purpose of the Study:
- To develop a user-friendly web application for Motif-HMM scanning to increase accessibility for the scientific community.
- To improve the performance of mHMM scanning through novel parametrization options.
Main Methods:
- Development of Leitmotif, a web application implementing mHMM scanning.
- Incorporation of an intuitive interface with extensive parametrization options.
- Introduction of two novel parameters to enhance performance.
Main Results:
- Leitmotif provides a widely accessible platform for mHMM scanning.
- Substantial improvements in performance, measured by ROC scores, were achieved.
- Leitmotif is currently the only available mHMM application.
Conclusions:
- Leitmotif democratizes the use of mHMM scanning for protein motif analysis.
- The application offers enhanced capabilities for discriminating protein sequences, especially those with motif variations.
- Leitmotif is freely available, promoting broader adoption in biological research.
Related Concept Videos
01:33Peptide Identification Using Tandem Mass Spectrometry
8.0K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
8.0K
01:33Proteomics
9.2K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
9.2K
02:04Protein-protein Interfaces
14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K