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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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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 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.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Updated: Jun 16, 2026

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

Efficient protein alignment algorithm for protein search.

Zaixin Lu1, Zhiyu Zhao, Bin Fu

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

BMC Bioinformatics
|February 4, 2010
PubMed
Summary
This summary is machine-generated.

We developed an efficient protein structure alignment algorithm for fast protein similarity searching. This tool accurately identifies structurally similar proteins from large databases like the Protein Data Bank (PDB).

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

Last Updated: Jun 16, 2026

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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein 3D conformations are crucial for inferring evolutionary relationships and classification.
  • Existing protein structure alignment algorithms face challenges in handling large datasets efficiently.
  • The exponential growth of protein structural data necessitates faster and more accurate alignment tools for classification and similarity searches.

Purpose of the Study:

  • To develop an efficient protein pairwise alignment algorithm.
  • To create a protein search tool that utilizes this algorithm for discovering similar protein structures.
  • To enable practical protein classification and similarity searches on large structural databases.

Main Methods:

  • Developed an efficient protein pairwise alignment algorithm.
  • Integrated the algorithm into a protein search tool.
  • Applied the tool to align query protein structures against the entire Protein Data Bank (PDB).

Main Results:

  • The algorithm aligns hundreds of protein structure pairs per second.
  • The search tool identifies similar structures from tens of thousands in the PDB within minutes on a single machine.
  • The tool demonstrates high accuracy in finding structurally similar proteins at SCOP family and superfamily levels, outperforming other systems.

Conclusions:

  • The developed algorithm is highly suitable for rapid protein structure searching.
  • The tool's speed and accuracy are competitive with existing protein search systems.
  • The pairwise alignment performance is comparable to established alignment algorithms.