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Related Concept Videos

Gene Families01:57

Gene Families

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...
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...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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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Analyzing and Building Nucleic Acid Structures with 3DNA
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PDBsum extras: SARS-CoV-2 and AlphaFold models.

Roman A Laskowski1, Janet M Thornton1

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

Protein Science : a Publication of the Protein Society
|November 15, 2021
PubMed
Summary
This summary is machine-generated.

PDBsum now offers detailed analyses of SARS-CoV-2 protein structures, including variants, and integrates AlphaFold models for human proteins. This enhances structural comparisons between predicted and experimental data.

Keywords:
3D protein structureAlphaFoldPDBPDBsumSARS-CoV-2protein databaseprotein structure analysisschematic diagrams

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • The Protein Data Bank (PDB) is a crucial resource for structural biology.
  • Analyzing and comparing protein structures is essential for understanding biological function and disease.
  • The PDBsum web server facilitates access to structural information.

Purpose of the Study:

  • To describe recent updates to the PDBsum web server.
  • To highlight the integration of SARS-CoV-2 protein structure analyses, including variants of concern.
  • To introduce the inclusion of AlphaFold models for human proteins and their comparison with experimental structures.

Main Methods:

  • PDBsum provides detailed structural analyses of PDB entries.
  • SARS-CoV-2 protein structures and variants are visualized on sequences and 3D models.
  • AlphaFold models for human proteins are incorporated and searchable via the Sequence Annotated by Structure (SAS) server.

Main Results:

  • PDBsum now offers comprehensive analyses of SARS-CoV-2 protein structures, aiding research on the virus.
  • The integration of AlphaFold models allows for direct comparison with experimentally determined protein structures.
  • The SAS server enables easy comparison of predicted protein models against existing PDB data.

Conclusions:

  • The updated PDBsum server enhances the study of viral proteins and human protein structures.
  • It provides valuable tools for comparing predicted protein models with experimental data.
  • PDBsum remains a freely accessible and valuable resource for the scientific community.