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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 Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
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...
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...

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Related Experiment Video

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Accelerating large-scale protein structure alignments with graphics processing units.

Bin Pang1, Nan Zhao, Michela Becchi

  • 1Informatics Institute, University of Missouri, Columbia, MO, USA.

BMC Research Notes
|February 24, 2012
PubMed
Summary
This summary is machine-generated.

We developed ppsAlign, a GPU-accelerated framework for fast and accurate protein structure alignment. This tool significantly speeds up large-scale structural bioinformatics analyses, overcoming computational challenges.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Last Updated: May 24, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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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

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biophysics

Background:

  • Large-scale protein structure alignment is crucial but computationally intensive.
  • Existing parallelization methods are costly and inaccessible.
  • Some methods sacrifice accuracy for speed by using simplified structure comparisons.

Purpose of the Study:

  • To present ppsAlign, a novel parallel protein structure alignment framework.
  • To leverage Graphics Processing Unit (GPU) parallelism for enhanced efficiency.
  • To enable accurate and rapid large-scale structure comparisons.

Main Methods:

  • Designed a parallel alignment framework (ppsAlign) optimized for GPUs.
  • Integrated concurrent alignment methods like TM-align and Fr-TM-align into the parallel design.
  • Evaluated performance on an NVIDIA Tesla C2050 GPU against CPU-based solutions.

Main Results:

  • Achieved a 36-fold speedup over TM-align.
  • Demonstrated a 65-fold speedup over Fr-TM-align.
  • Observed a 40-fold speedup compared to MAMMOTH.

Conclusions:

  • ppsAlign offers high-performance protein structure alignment.
  • Effectively addresses computational complexity in structural bioinformatics.
  • Enables large-scale structure comparisons using GPU parallel computing power.