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Related Concept Videos

Protein Families02:47

Protein Families

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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...
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Gene Families01:57

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Globular and Fibrous Proteins02:21

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
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Protein Organization01:24

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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.
The primary structure of a protein is its amino acid sequence....
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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PDBsum: Structural summaries of PDB entries.

Roman A Laskowski1, Jagoda Jabłońska2, Lukáš Pravda3

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.

Protein Science : a Publication of the Protein Society
|September 7, 2017
PubMed
Summary

PDBsum provides comprehensive structural analyses for Protein Data Bank (PDB) entries, offering insights into protein structures and interactions. This web server enhances structural data accessibility and visualization for researchers worldwide.

Keywords:
3D protein structurePDBPDBsumenzymesmolecular interactionsprotein databaseprotein structure analysisschematic diagrams

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • The Protein Data Bank (PDB) is a crucial repository for macromolecular structure data.
  • Accessing and interpreting complex structural information from the PDB can be challenging for researchers.
  • There is a need for user-friendly tools that provide comprehensive analyses of PDB entries.

Purpose of the Study:

  • To introduce PDBsum, a web server designed to offer detailed structural information and analyses for PDB entries.
  • To provide researchers with an accessible platform for visualizing and understanding protein structures and their interactions.
  • To enable users to upload and analyze their own PDB files.

Main Methods:

  • Web server development utilizing image-based analyses.
  • Integration of tools for protein secondary structure identification.
  • Inclusion of analyses for protein-ligand and protein-DNA interactions.
  • Incorporation of structural quality assessment using PROCHECK.
  • Interactive 3D structure visualization using RasMol, PyMOL, and 3Dmol.js.

Main Results:

  • PDBsum offers a wide array of structural analyses, including secondary structure, interaction data, and quality assessments.
  • Interactive 3D visualization tools allow for dynamic exploration of protein structures.
  • Users can upload custom PDB files for personalized, password-protected analyses.
  • The server provides freely accessible structural information for numerous PDB entries.

Conclusions:

  • PDBsum serves as a valuable resource for structural biologists and researchers by simplifying the interpretation of PDB data.
  • The web server enhances the accessibility and utility of macromolecular structural information.
  • PDBsum facilitates a deeper understanding of protein structure-function relationships through comprehensive analyses and visualization.