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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...
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 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

Accelerated protein structure comparison using TM-score-GPU.

Ling-Hong Hung1, Ram Samudrala

  • 1Department of Microbiology, University of Washington, Seattle, WA 98195-7735, USA.

Bioinformatics (Oxford, England)
|June 22, 2012
PubMed
Summary
This summary is machine-generated.

A new Graphical Processing Unit (GPU) implementation, TM-score-GPU, significantly accelerates protein structure comparisons. This faster method enables efficient large-scale analysis in structural biology and protein structure prediction.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Root-mean-square-deviation (RMSD) is a common but limited measure for protein structure similarity.
  • Global RMSD can be skewed by protein length and divergent loops, obscuring local similarities.
  • Template Modeling (TM)-score offers a more robust measure but is computationally intensive.

Purpose of the Study:

  • To develop a significantly faster method for calculating TM-score.
  • To enable efficient large-scale protein structure comparisons and analyses.
  • To facilitate applications like protein model clustering and genome-wide structure comparisons.

Main Methods:

  • Implemented a fast TM-score version for Graphical Processing Units (TM-score-GPU).
  • Utilized a novel hybrid Kabsch/quaternion method for optimal superposition and RMSD calculation, optimized for parallel processing.
  • The implementation is in C++/OpenCL.

Main Results:

  • TM-score-GPU demonstrated a 68-fold speed increase compared to the CPU implementation on an ATI 5870 GPU.
  • The method was successfully applied to over 3 million comparisons across six model sets.
  • The software, including GPU code and hybrid RMSD subroutine, is available for unrestricted use.

Conclusions:

  • TM-score-GPU provides a substantial computational speedup for TM-score calculations.
  • This acceleration makes TM-score practical for large-scale structural biology applications.
  • The efficient computation facilitates advanced analyses in protein structure prediction and functional annotation.