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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

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
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Related Experiment Video

Updated: Jun 13, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

SeqRate: sequence-based protein folding type classification and rates prediction.

Guan Ning Lin1, Zheng Wang, Dong Xu

  • 1Informatics Institute, University of Missouri, Columbia, 65211, USA. guanlin@mail.missouri.edu

BMC Bioinformatics
|May 5, 2010
PubMed
Summary
This summary is machine-generated.

SeqRate predicts protein folding kinetic type and folding rates using only protein sequence data. This sequence-based approach improves accuracy over previous methods for protein folding prediction.

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Last Updated: Jun 13, 2026

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16:41

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Published on: November 3, 2011

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational Biology
  • Biophysics
  • Protein Science

Background:

  • Protein folding rate is crucial for protein function and design.
  • Existing prediction methods often require tertiary structure and do not differentiate folding kinetics.
  • Accurate prediction of protein folding properties is essential for understanding biological processes.

Purpose of the Study:

  • To develop a sequence-based method for predicting protein folding kinetic type (two-state vs. multi-state) and real-valued folding rates.
  • To overcome limitations of structure-dependent prediction methods.
  • To provide a tool for analyzing protein folding dynamics from sequence alone.

Main Methods:

  • Developed SeqRate, a method utilizing sequence length, amino acid composition, contact order, contact number, and predicted secondary structure.
  • Employed support vector machines for classification and regression tasks.
  • Systematically analyzed feature contributions to prediction accuracy.

Main Results:

  • Achieved 80% accuracy in classifying protein folding kinetic types.
  • Obtained high Pearson correlation coefficients (0.81 for two-state, 0.80 for three-state) and low mean absolute differences for folding rate prediction.
  • SeqRate is the first sequence-based method for folding type classification, outperforming prior sequence-based approaches.

Conclusions:

  • SeqRate offers an accurate, sequence-based approach to predict protein folding kinetics and rates.
  • The method demonstrates improved performance over existing sequence-based techniques.
  • Web server and software are publicly available for broader research use.