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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 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 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...

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Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
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Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

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Protein structure modeling for CASP10 by multiple layers of global optimization.

Keehyoung Joo1, Juyong Lee, Sangjin Sim

  • 1Center for In Silico Protein Science, Korea Institute for Advanced Study, Dongdaemun-gu, Seoul, 130-722, Korea; Center for Advanced Computation, Korea Institute for Advanced Study, Dongdaemun-gu, Seoul, 130-722, Korea.

Proteins
|August 23, 2013
PubMed
Summary

A new protein modeling system (PMS) enhances structural accuracy using conformational space annealing (CSA) and a novel energy function. This template-based modeling approach significantly improves side-chain prediction accuracy in protein structure generation.

Keywords:
CASPenergy functionglobal optimizationhigh-accuracy modelinghomology modelingside-chain modelingstructure predictiontemplate-based modeling

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Template-based modeling (TBM) is a key method for protein structure prediction.
  • Existing TBM protocols face challenges in accurately modeling side-chains and regions lacking template information.

Purpose of the Study:

  • To introduce a novel protein modeling system (PMS) for enhanced accuracy in protein structure prediction.
  • To improve both backbone and side-chain modeling within the TBM framework.

Main Methods:

  • Developed a new protein modeling system (PMS) integrating multiple stages of template-based modeling.
  • Applied conformational space annealing (CSA) global optimization to sequence-structure alignment, 3D chain building, and side-chain remodeling.
  • Introduced a new energy function for 3D chain building, incorporating Lorentzian-type distance restraints and physical energy terms (DFA, DFIRE, hydrogen bonding).
  • Developed a random forest machine learning algorithm for quality assessment of templates, alignments, and models.

Main Results:

  • The PMS protocol demonstrated improved modeling accuracy at each stage of its application.
  • The integration of CSA optimization and quality assessment led to significant gains in protein structure prediction.
  • Final PMS models showed substantially higher accuracy in side-chain modeling compared to intermediate steps.

Conclusions:

  • The developed protein modeling system (PMS) effectively enhances protein structure prediction accuracy, particularly for side-chains.
  • The combination of CSA global optimization, a novel energy function, and machine learning-based quality assessment represents a significant advancement in template-based modeling.