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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 Organization01:13

Protein Organization

Overview
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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

Integrated search and alignment of protein structures.

Ahmet Sacan1, I Hakki Toroslu, Hakan Ferhatosmanoglu

  • 1Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. sacan@cse.ohio-state.edu

Bioinformatics (Oxford, England)
|October 24, 2008
PubMed
Summary

Vorometric efficiently searches and aligns three-dimensional (3D) protein structures within large databases. This new method improves retrieval accuracy and alignment quality compared to existing tools.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biochemistry

Background:

  • Protein structure databases are growing rapidly, increasing the challenge of identifying similar structures.
  • Existing methods for protein structure comparison face scalability issues.
  • Efficient search and alignment are crucial for understanding protein function and evolution.

Purpose of the Study:

  • To introduce Vorometric, a novel method for efficient search and alignment of protein structures.
  • To address the dual challenges of retrieval and alignment in structural bioinformatics.
  • To provide a web service for accessing the Vorometric method.

Main Methods:

  • Utilizes Voronoi contacts enriched with secondary structure information.
  • Employs a metric substitution matrix for efficient indexing.
  • Extends contact hits to identify high-scoring segment pairs for structural alignment.

Main Results:

  • Vorometric effectively retrieves similar protein structures and produces high-quality alignments.
  • The method identifies cross-fold similarities and outperforms current retrieval methods in accuracy.
  • Structural superpositions generated by Vorometric show superior quality and coverage.

Conclusions:

  • Vorometric offers an effective solution for searching and aligning protein structures.
  • The method demonstrates improved accuracy and alignment quality over existing tools.
  • Vorometric is accessible as a web service for broader research use.