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Related Concept Videos

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.
Protein Organization01:13

Protein Organization

Overview
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.
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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

Updated: May 24, 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

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

Dong Xu1, Yang Zhang

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.

Proteins
|March 14, 2012
PubMed
Summary
This summary is machine-generated.

QUARK, a novel protein structure prediction program, successfully models protein folds without templates. This computational biology tool advances ab initio protein folding by assembling structures from fragments, showing promise for complex biological modeling.

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Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Ab initio protein folding is a complex challenge in computational biology.
  • Difficulties arise from force field design and conformational search.

Purpose of the Study:

  • To develop a novel program, QUARK, for template-free protein structure prediction.
  • To improve the efficiency and accuracy of ab initio protein folding predictions.

Main Methods:

  • QUARK breaks query sequences into fragments (1-20 residues).
  • Fragment structures are retrieved from experimental data.
  • Replica-exchange Monte Carlo simulations assemble full-length models.
  • A composite knowledge-based force field guides the simulations, incorporating novel energy terms and Monte Carlo movements.

Main Results:

  • QUARK successfully constructs 3D models of correct folds in one-third of short proteins (up to 100 residues) without using global templates.
  • The QUARK server outperformed other leading servers in the ninth Critical Assessment of protein Structure Prediction (CASP9) experiment.
  • Performance was measured by cumulative Z-score of global distance test-total scores in the FM category.

Conclusions:

  • QUARK demonstrates significant progress in template-free protein structure prediction.
  • The developed methods enhance both the force field and search engine efficiency.
  • These advancements contribute to solving the challenging problem of ab initio protein folding.