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Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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

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Related Experiment Video

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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

OnD-CRF: predicting order and disorder in proteins using [corrected] conditional random fields.

Lixiao Wang1, Uwe H Sauer

  • 1Umeå Centre for Molecular Pathogenesis, UCMP, and Centre for Chemical Biology, KBC, Umeå University, SE-901 87 Umeå, Sweden.

Bioinformatics (Oxford, England)
|April 24, 2008
PubMed
Summary
This summary is machine-generated.

A new method called Order and Disorder prediction using Conditional Random Fields (OnD-CRF) accurately predicts protein structure transitions. This protein disorder prediction model ranked highest among automatic servers in benchmarking tests.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Predicting protein structural transitions is crucial for understanding protein function.
  • Existing methods face challenges in accurately distinguishing ordered and disordered regions.

Purpose of the Study:

  • To introduce and evaluate a novel method, Order and Disorder prediction using Conditional Random Fields (OnD-CRF), for predicting protein structural transitions.
  • To assess the performance of OnD-CRF against established criteria and benchmarks.

Main Methods:

  • Developed the OnD-CRF method utilizing Conditional Random Fields (CRFs).
  • Features for the CRFs are derived from amino acid sequences and predicted secondary structures.
  • Benchmarked performance using CASP7 targets and CASP evaluation criteria.

Main Results:

  • OnD-CRF demonstrates high accuracy in predicting transitions between structured and disordered protein regions.
  • The OnD-CRF model achieved the top rank among fully automatic servers in benchmarking.
  • The method effectively integrates sequence and secondary structure information for prediction.

Conclusions:

  • OnD-CRF represents a significant advancement in predicting protein order and disorder.
  • The method's high performance suggests its utility in structural bioinformatics and drug discovery.
  • OnD-CRF is a valuable tool for researchers studying protein dynamics and function.