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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 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...
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...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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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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

Template-based protein structure modeling using TASSER(VMT.).

Hongyi Zhou1, Jeffrey Skolnick

  • 1Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318.

Proteins
|November 23, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces TASSER(VMT), a novel protein structure modeling method using a variable number of multiple templates. This approach significantly improves protein structure prediction accuracy compared to previous methods.

Keywords:
SP3TASSERalignmenttemplate-based modelingthreading

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Template-based modeling is a common approach for protein structure prediction.
  • Multiple templates often yield better results than single templates.

Purpose of the Study:

  • To develop and evaluate TASSER(VMT), a new variant of TASSER utilizing a variable number of multiple templates for enhanced protein structure modeling.
  • To improve target-template alignment algorithms for more accurate structural predictions.

Main Methods:

  • Developed the SP(3) alternative alignment algorithm combining parametric alignment and knowledge-based refinement.
  • Integrated SP(3) threading, SP(3) alternative, and HHEARCH alignments.
  • Grouped template models into sets with variable template/alignment combinations and ran short TASSER simulations.
  • Pooled models from all sets, selected top candidates using FTCOM ranking, and performed a final long TASSER refinement.

Main Results:

  • TASSER(VMT) achieved average GDT-TS score improvements of 3.5% (easy) and 4.3% (hard) targets over pro-sp(3)-TASSER.
  • On CASP9 targets, improvements were 8.2% (easy) and 9.3% (hard) compared to pro-sp3-TASSER.
  • Outperformed top-ranked CASP9 methods like Zhang-Server, QUARK, and HHpredA.

Conclusions:

  • TASSER(VMT) represents a significant advancement in template-based protein structure modeling.
  • The method demonstrates superior accuracy and performance in predicting protein structures.
  • The program is publicly available for download, facilitating further research.