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Protein Folding

Protein 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
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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.
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Updated: Apr 25, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

PconsFold: improved contact predictions improve protein models.

Mirco Michel¹, Sikander Hayat², Marcin J Skwark²

¹Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden, Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden, Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

Bioinformatics (Oxford, England)

|August 28, 2014

Summary

This summary is machine-generated.

Improved protein contact prediction using PconsFold and PconsC enhances protein structure prediction accuracy. This study quantifies the significant improvements in TM-scores and model quality achieved with these advanced methods.

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Published on: July 14, 2015

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Protein contact prediction quality is crucial for accurate protein structure prediction.
Recent advancements allow separation of direct and indirect evolutionary information to improve contact prediction.
Improved contact prediction methods can potentially enhance de novo protein structure prediction.

Purpose of the Study:

To evaluate the impact of improved protein contact prediction methods on the accuracy of protein structure prediction.
To quantify the performance gains using PconsFold and PconsC compared to earlier methods.

Main Methods:

Utilized PconsFold, an automated pipeline for ab initio protein structure prediction.
Employed PconsC for enhanced contact prediction, integrated with the Rosetta folding protocol.
Benchmarked performance on small (15 proteins) and larger datasets.

Main Results:

PconsFold improved TM-scores by an average of 33% compared to the original EVfold.
PconsC-based predictions showed 15-30% quality improvement over previous contact prediction techniques.
Rosetta improved model chemistry compared to CNS, without significant global accuracy gains.

Conclusions:

Enhanced protein contact prediction significantly improves de novo protein structure prediction accuracy.
PconsFold and PconsC represent substantial advancements in computational protein structure prediction.
The modularity of PconsFold allows for easy integration of future contact prediction improvements.