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Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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...
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...
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: Jun 29, 2026

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

CPDB: a database of circular permutation in proteins.

Wei-Cheng Lo1, Chi-Ching Lee, Che-Yu Lee

  • 1Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.

Nucleic Acids Research
|October 10, 2008
PubMed
Summary

Circular permutation (CP) in proteins, where the sequence is circularized and termini are relocated, typically maintains native structure and function. A new database, CPDB, now provides a centralized resource for studying these circular permutants.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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Last Updated: Jun 29, 2026

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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Circular permutation (CP) involves altering protein termini after circularizing the sequence.
  • CPs often retain native protein structures and functions, with potential for enhanced stability or novel functions.
  • Previous research on CPs was limited by the lack of comprehensive, large-scale data collections.

Purpose of the Study:

  • To introduce CPDB, the first comprehensive database for circular permutation in proteins.
  • To establish a hierarchical organization for CP data, facilitating analysis and comparison.
  • To provide tools for CP identification, characterization, prediction, and visualization.

Main Methods:

  • Development of CPDB with a hierarchical data structure (CP clusters, folds, classes).
  • Integration of tools for CP identification, characterization, comparison, and visualization.
  • Implementation and assessment of multiple CP site prediction methods within the database.

Main Results:

  • CPDB offers a structured repository of circular permutation information.
  • The database includes integrated computational tools for CP analysis.
  • Several CP site prediction methods have been evaluated and made accessible through CPDB.

Conclusions:

  • CPDB serves as a valuable resource for protein folding, evolution, and structural studies.
  • The database facilitates the discovery of new protein relationships and the engineering of novel CPs.
  • CPDB supports research in biotechnical and industrial applications of circularly permuted proteins.