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Related Concept Videos

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...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
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 Organization01:24

Protein 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.
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Protein and Protein Structures02:15

Protein and Protein Structures

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...

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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

A sampling-based method for ranking protein structural models by integrating multiple scores and features.

Xiaohu Shi1, Jingfen Zhang, Zhiquan He

  • 1College of Computer Science and Technology, Jilin University, Jilin, Changchun 130012, China.

Current Protein & Peptide Science
|July 27, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a machine learning method to improve protein structure quality assessment. The new approach effectively ranks protein models, outperforming existing scoring functions for better model selection.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Machine Learning

Background:

  • Protein tertiary structure prediction is crucial but selecting high-quality models from numerous candidates remains a significant challenge.
  • Existing protein structure prediction tools often generate many models but struggle with accurate quality assessment and best model selection.

Purpose of the Study:

  • To develop an advanced sampling-based machine learning method for ranking protein structural models.
  • To enhance the accuracy of protein structure quality assessment and improve the selection of the best structural models.

Main Methods:

  • Integrated multiple scores and features using two Radial Basis Function (RBF) models trained on different datasets.
  • Combined RBF scores with five established scoring functions (Opus-CA, Opus-PSP, DFIRE, RAPDF, Cheng Score) via a sampling method.
  • Employed an additional RBF model to rank structural models based on sampling distribution features.

Main Results:

  • The proposed method was evaluated on CASP8 server prediction models and in-house MUFOLD-generated models.
  • Demonstrated superior performance in best model selection compared to individual scoring functions.
  • Achieved a better overall correlation between predicted and actual structural quality rankings.

Conclusions:

  • The developed sampling-based machine learning approach significantly improves protein structure quality assessment.
  • This method offers a more reliable way to select the best protein models from large sets of predicted structures.
  • The findings suggest a promising direction for advancing protein structure prediction accuracy.