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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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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 12, 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

PCBOST: Protein classification based on structural trees.

Alexey B Gordeev1, Anton M Kargatov, Alexander V Efimov

  • 1Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation.

Biochemical and Biophysical Research Communications
|June 25, 2010
PubMed
Summary

We introduce protein classification based on structural trees (PCBOST), a new method grouping proteins by structural similarity and folding pathways. This protein classification database currently includes 3847 proteins and domains.

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Last Updated: Jun 12, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

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Published on: November 3, 2011

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

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:

  • Protein classification is crucial for understanding biological functions.
  • Existing methods often rely on sequence or function, not solely structure.
  • A comprehensive structural classification can reveal novel relationships.

Purpose of the Study:

  • To present a novel hierarchical protein classification system based on structural similarity.
  • To introduce the Protein Classification Based on Structural Trees (PCBOST) database.
  • To categorize proteins using fold similarity and modeled folding pathways.

Main Methods:

  • Developing a hierarchical classification system (PCBOST).
  • Analyzing protein structures for overall fold similarity.
  • Modeling protein folding pathways to infer relationships.
  • Excluding amino acid sequences, functions, and evolutionary data from classification.

Main Results:

  • The PCBOST database currently contains 3847 proteins and domains.
  • Proteins are grouped into six categories based on structural similarity.
  • These categories form six distinct structural trees, encompassing 10,547 PDB entries.
  • Ongoing work aims to extend the database and create new structural trees.

Conclusions:

  • PCBOST offers a unique, structure-centric approach to protein classification.
  • The classification highlights similarities in protein folding mechanisms.
  • The database provides a valuable resource for structural bioinformatics research.