Related Experiment Video
Updated: May 21, 2026
08:48
Specificity Analysis of Protein Lysine Methyltransferases Using SPOT Peptide Arrays
Published on: November 29, 2014
Prediction of lysine post-translational modifications using bioinformatic tools
1Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269-3156, U.S.A. daniel.schwartz@uconn.edu
Essays in Biochemistry
|June 20, 2012
Summary
Many lysine post-translational modification prediction tools fail to perform reliably. Researchers should critically evaluate these computational tools, as most do not outperform random chance in identifying acetylation, methylation, SUMOylation, and ubiquitination sites.
Area of Science:
- Biochemistry
- Bioinformatics
- Proteomics
Background:
- Lysine post-translational modifications (PTMs) are crucial for protein function.
- Experimental tools for PTM detection have advanced, but many sites remain undiscovered.
- Computational tools can aid in predicting lysine PTM sites.
Purpose of the Study:
- To assess the performance of online computational tools for predicting lysine PTMs.
- To evaluate the reliability of existing prediction software for researchers.
Main Methods:
- Surveyed 11 online computational tools for predicting lysine PTMs.
- Utilized unbiased testing datasets to evaluate tool performance.
- Assessed metrics including sensitivity and specificity.
Main Results:
- Nine out of 11 tools performed no better than random chance.
- Several tools exhibited high false-positive rates, rendering them unusable.
- Reported performance metrics often contradicted actual performance on unbiased data.
Conclusions:
- Most currently available lysine PTM prediction tools are unreliable.
- Researchers must exercise caution when using these tools for hypothesis generation.
- Further development and rigorous validation of prediction software are needed.
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02:04Covalently Linked Protein Regulators
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
These groups modify specific amino acids in a protein.
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:32Histone Modification
The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...