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Related Concept Videos

Protein Organization01:24

Protein Organization

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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.
The primary structure of a protein is its amino acid sequence....
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Protein Folding Quality Check in the RER01:29

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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...
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Protein and Protein Structure02:15

Protein and Protein Structure

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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.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein and Protein Structures02:15

Protein and Protein Structures

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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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QAcon: single model quality assessment using protein structural and contact information with machine learning

Renzhi Cao1, Badri Adhikari2, Debswapna Bhattacharya3

  • 1Department of Computer Science, Pacific Lutheran University, WA 98447, USA.

Bioinformatics (Oxford, England)
|December 31, 2016
PubMed
Summary

We developed QAcon, a novel single-model protein quality assessment method. QAcon utilizes structural features and contact predictions, outperforming other methods in CASP11 benchmarks.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein model quality assessment (QA) is crucial for protein structure prediction.
  • Existing consensus QA methods can fail with many low-quality models.
  • Single-model QA methods are needed for reliable assessment.

Purpose of the Study:

  • To develop a novel single-model quality assessment method named QAcon.
  • To improve the accuracy of protein model quality evaluation.
  • To leverage residue contact predictions for enhanced QA.

Main Methods:

  • Developed QAcon, a single-model QA method.
  • Utilized structural features, physicochemical properties, and residue contact predictions.
  • Trained a two-layer neural network on CASP9 data with 12 features, including a novel contact prediction score.

Main Results:

  • QAcon was blindly benchmarked on the CASP11 dataset.
  • QAcon ranked among the top single-model QA methods.
  • Features based on contact prediction demonstrated significant value for QA.

Conclusions:

  • QAcon is a highly effective single-model protein QA method.
  • Contact prediction features are valuable for assessing protein model quality.
  • The developed method offers a reliable alternative to consensus QA.