Related Experiment Video
Updated: Aug 3, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Protein secondary structure: entropy, correlations and prediction
Gavin E Crooks1, Steven E Brenner
1Department of Plant and Microbial Biology, University of California, 111 Koshland Hall No. 3102, Berkeley, CA 94720-3102, USA. gec@compbio.berkeley.edu
Bioinformatics (Oxford, England)
|February 28, 2004
Summary
Protein secondary structure is mainly determined by local interactions. Current prediction algorithms are nearly optimal, with limited room for improvement in predicting protein folding.
Area of Science:
- Biochemistry
- Computational Biology
- Structural Biology
Background:
- Investigating the primary drivers of protein secondary structure determination.
- Distinguishing between local and non-local interactions in protein folding.
Purpose of the Study:
- To quantify the contribution of local versus non-local interactions to protein secondary structure.
- To assess the information content of local residue correlations for secondary structure prediction.
Main Methods:
- Measuring entropy densities of primary and secondary structure sequences.
- Calculating local inter-sequence mutual information density.
Main Results:
- Short-range interactions are crucial for protein secondary structure.
- Neighboring amino acid correlations provide minimal information for secondary structure prediction.
- Local correlations account for only one-fourth of the information needed for secondary structure determination.
Conclusions:
- Protein folding is a cooperative process involving concurrent formation of secondary and tertiary structures.
- Existing single-sequence secondary structure prediction methods are near-optimal.
- Significant improvements in prediction accuracy are unlikely with current approaches.
Related Concept Videos
01:13Protein Organization
Overview
01:22Protein Folding
Overview
01:13Protein Organization
Overview
01:22Protein Folding
Overview
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:25Protein Folding
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...