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Updated: Jul 21, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A combined algorithm for genome-wide prediction of protein function.
E M Marcotte1, M Pellegrini, M J Thompson
1Molecular Biology Institute, UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles 90095, USA.
Nature
|November 26, 1999
Summary
Researchers mapped yeast protein functions by analyzing correlated evolution, gene expression, and domain fusion. This identified over 93,000 functional links, assigning functions to over half of previously uncharacterized yeast proteins.
Area of Science:
- Proteomics
- Bioinformatics
- Systems Biology
Background:
- Advancements in genomics enable novel approaches to protein function and interaction discovery.
- Understanding protein networks is crucial for deciphering cellular mechanisms.
Purpose of the Study:
- To identify functional relationships among Saccharomyces cerevisiae proteins.
- To assign functions to previously uncharacterized yeast proteins.
Main Methods:
- Proteins were grouped based on correlated evolution.
- Messenger RNA expression patterns were analyzed for correlations.
- Patterns of protein domain fusion were examined.
- Functional links were inferred from these integrated data.
Main Results:
- Over 93,000 pairwise links between functionally related yeast proteins were discovered.
- Functional roles were assigned to over 50% of previously uncharacterized yeast proteins (2,557 proteins).
- Specific examples include a novel protein family, a cancer-related protein homolog, and the yeast prion Sup35.
Conclusions:
- Integrated analysis of evolutionary, expression, and structural data effectively reveals protein functional networks.
- This approach significantly enhances the annotation of proteomes, particularly for uncharacterized proteins.
- The identified links provide a foundation for further experimental validation and biological discovery.
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02:26Conservation of Protein Domains Over Different Proteins
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02:04Protein-protein Interfaces
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02:26Protein Networks
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03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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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.
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