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Related Concept Videos

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 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 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 Organization01:24

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

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Related Experiment Video

Updated: Jun 20, 2026

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

Search similar protein structures with classification, sequence and 3d alignments.

Zaixin Lu1, Zhiyu Zhao, Sergio Garcia

  • 1Department of Computer Science, University of Texas-Pan American, Edinburg, TX 78539, USA. lzaixin@broncs.utpa.edu

Journal of Bioinformatics and Computational Biology
|September 29, 2009
PubMed
Summary
This summary is machine-generated.

We created a new algorithm and web tool for finding similar protein structures in the Protein Data Bank (PDB). This tool is more accurate and faster than existing systems for protein structure comparison.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Related Experiment Videos

Last Updated: Jun 20, 2026

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

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

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • The Protein Data Bank (PDB) contains a vast repository of protein structures.
  • Efficiently searching and comparing these structures is crucial for understanding protein function and evolution.

Purpose of the Study:

  • To develop and present a novel algorithm and web tool for searching similar protein structures within the PDB.
  • To offer a more accurate and efficient method for protein structure comparison.

Main Methods:

  • The algorithm integrates protein classification, geometric feature extraction, sequence alignment, and 3D structure alignment.
  • A web tool provides an accessible interface for users to query the PDB for similar structures.

Main Results:

  • The developed tool demonstrates superior accuracy compared to established systems like PSI-BLAST, 3D-BLAST, and SSM in identifying structurally similar proteins.
  • The search speed is competitive with existing protein structure search systems.

Conclusions:

  • The new algorithm and web tool offer a powerful and efficient solution for protein structure similarity searches.
  • This resource facilitates the discovery of structurally related proteins within the PDB, aiding biological research.