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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 Organization01:24

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 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...
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: 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

Exploring protein structural dissimilarity to facilitate structure classification.

Pooja Jain1, Jonathan D Hirst

  • 1School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, UK. pcxpj1@nottingham.ac.uk

BMC Structural Biology
|September 22, 2009
PubMed
Summary
This summary is machine-generated.

A new dissimilarity coefficient, Omega, improves protein structure classification by enhancing the true positive rate for identifying shared protein families and folds within the Structural Classification of Proteins (SCOP) database.

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Last Updated: Jun 20, 2026

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Published on: July 16, 2017

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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 structure classification is crucial for understanding protein relationships.
  • Automating the classification process for databases like SCOP is a key research area.
  • Accurate classification aids in predicting protein function and evolutionary history.

Purpose of the Study:

  • To develop and evaluate a novel method for predicting the deepest SCOP structural level shared between unclassified and classified proteins.
  • To compare the performance of the new method against existing tools like DaliLite Z score.

Main Methods:

  • Computation of a dissimilarity coefficient (Omega) using structural and sequence-based descriptors of secondary structure elements (SSEs).
  • Evaluation of Omega's performance in predicting shared SCOP Class, Fold, Super-family, and Family levels.
  • Comparison of Omega with DaliLite Z score on datasets with varying sequence identities and domain sizes.

Main Results:

  • Omega demonstrated a greater than four-fold increase in true positive rate (TPR) for predicting shared Family levels compared to DaliLite Z score.
  • Omega showed higher sensitivity in predicting common Fold levels and slightly better performance for Super-family levels.
  • Omega's performance was comparable to DaliLite Z score for predicting Class and Fold levels.

Conclusions:

  • The Omega coefficient shows significant potential for improving automated protein structure classification in SCOP.
  • Omega may be a more effective measure than DaliLite Z score for classifying proteins to deeper hierarchical levels.
  • Further refinement is needed, particularly for comparing structures with unequal numbers of SSEs.