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Related Concept Videos

Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
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...
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...
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 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...

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Related Experiment Video

Updated: Jul 1, 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

Using the blocks database to recognize functional domains.

Jorja G Henikoff1, Elizabeth A Greene, Nick Taylor

  • 1Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

Current Protocols in Bioinformatics
|September 17, 2008
PubMed
Summary
This summary is machine-generated.

The Blocks Database organizes conserved protein sequence segments for identifying protein families. It provides tools for sequence analysis, family comparison, and designing PCR primers for homologous sequence isolation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Protein sequence analysis is crucial for understanding protein function and evolution.
  • Identifying conserved regions within protein families aids in classification and functional prediction.

Purpose of the Study:

  • To introduce the Blocks Database as a resource for protein family analysis.
  • To describe tools for utilizing blocks in sequence comparison and discovery.

Main Methods:

  • Utilizing ungapped multiple sequence alignments to define conserved protein regions (blocks).
  • Developing and applying Blocks-based tools for database searching and relationship exploration.
  • Methods for creating new blocks and designing PCR primers from existing blocks.

Main Results:

  • The Blocks Database provides a structured collection of conserved protein segments.
  • Blocks-based tools enable efficient searching, phylogenetic analysis, and primer design.
  • The database facilitates the identification of homologous sequences and protein family relationships.

Conclusions:

  • The Blocks Database is a valuable resource for protein sequence analysis and family identification.
  • Blocks-based tools offer a comprehensive approach to exploring protein sequence data.
  • This resource supports molecular biology research through sequence comparison and targeted gene isolation.