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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 Organization01:13

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 Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Searching protein 3-D structures in linear time.

Tetsuo Shibuya1

  • 1Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan. tshibuya@hgc.jp

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 10, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces faster algorithms for searching protein 3-D structures in large databases. The new methods significantly improve the speed of finding similar molecular substructures using root mean square deviation (RMSD).

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Molecular modeling

Background:

  • Post-genomic molecular biology heavily relies on analyzing protein three-dimensional (3-D) structures.
  • Searching large 3-D structure databases is crucial for molecular biology research.
  • Root mean square deviation (RMSD) is the standard metric for comparing molecular structure similarity.

Purpose of the Study:

  • To develop faster algorithms for identifying protein substructures within a database that match a query structure within a specified RMSD threshold.
  • To improve upon existing time complexities for substructure searching in protein structure databases.
  • To provide practical speedups for real-world applications using large-scale biological data.

Main Methods:

  • Development of new theoretically and practically efficient algorithms for substructure searching based on RMSD.
  • Introduction of a novel linear-expected-time algorithm, offering a theoretical breakthrough.
  • Design of preprocessing algorithms to further accelerate query times for large databases.

Main Results:

  • The new linear-expected-time algorithm significantly outperforms previous methods.
  • Experimental results on the Protein Data Bank (PDB) show 3.6-28 times faster performance compared to existing algorithms for RMSD searches within 1Å.
  • Preprocessing algorithms offer improved query time complexities, with one achieving O(m + N sqrt(m)) expected query time.

Conclusions:

  • The proposed algorithms represent a significant advancement in the efficiency of 3-D protein structure analysis and database searching.
  • The practical speedups demonstrated are substantial, making large-scale structural comparisons more feasible.
  • These advancements facilitate more effective exploration of molecular structures and their relationships.