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Updated: Jun 20, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
In Silico screening for functional candidates amongst hypothetical proteins
Claus Desler1, Prashanth Suravajhala, May Sanderhoff
1Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde, Denmark. cdesler@ruc.dk
BMC Bioinformatics
|September 17, 2009
Summary
This study introduces an in silico method to identify expressed hypothetical proteins, significantly improving the prediction of proteins with mitochondrial roles. This tool aids researchers in prioritizing candidates for experimental validation.
Area of Science:
- Proteomics
- Bioinformatics
Background:
- Hypothetical proteins, predicted but unverified, form a large part of eukaryotic proteomes.
- Distinguishing expressed hypothetical proteins from pseudogene products is crucial for understanding cellular functions.
Purpose of the Study:
- To develop and validate an in silico strategy for identifying expressed hypothetical proteins.
- To specifically pinpoint hypothetical proteins with a high probability of having a biological function, particularly in mitochondria.
Main Methods:
- An in silico selection strategy was developed, sorting hypothetical proteins based on subcellular targeting signals and characterized protein domains.
- The strategy was validated using a human hypothetical protein database from 2006, comparing predictions with experimentally verified protein status in 2008.
Main Results:
- The in silico strategy successfully predicted expressed hypothetical proteins, with a notable enrichment for mitochondrial proteins.
- Among proteins predicted to have mitochondrial roles, 53-62% were experimentally characterized by 2008, with 85% of those assigned a mitochondrial function.
Conclusions:
- The developed in silico strategy effectively identifies promising hypothetical proteins for further experimental investigation.
- This approach significantly enhances the efficiency of discovering functional proteins, especially those involved in mitochondrial biology.
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