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Related Concept Videos

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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.
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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.
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Investigating Protein Structure and Evolution with SCOP2.

Antonina Andreeva1, Dave Howorth1, Cyrus Chothia1

  • 1MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom.

Current Protocols in Bioinformatics
|March 11, 2015
PubMed
Summary
This summary is machine-generated.

SCOP2 offers an advanced framework for protein classification, organizing structures by evolutionary and structural relationships. This database provides tools like SCOP2-Browser for exploring protein groupings.

Keywords:
protein evolutionprotein structuresequence-structure relationship

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • The Structural Classification of Proteins (SCOP) database has been a foundational resource for organizing proteins.
  • A need exists for a more advanced framework to classify proteins based on evolving structural and evolutionary data.

Purpose of the Study:

  • To introduce SCOP2, a successor to SCOP, offering an advanced protein classification system.
  • To describe the structure and accessibility of the SCOP2 database and its classification system.

Main Methods:

  • Utilizing a directed acyclic graph to represent protein relationships.
  • Developing SCOP2-Browser and SCOP2-Graph for data exploration.

Main Results:

  • SCOP2 provides a refined classification of proteins based on structural and evolutionary relationships.
  • The SCOP2 data are accessible through user-friendly interfaces for investigation.

Conclusions:

  • SCOP2 represents a significant advancement in protein structural and evolutionary classification.
  • The database facilitates deeper exploration of protein relationships and groupings.