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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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PDBe: improved findability of macromolecular structure data in the PDB
David R Armstrong1, John M Berrisford1, Matthew J Conroy1
1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nucleic Acids Research
|November 7, 2019
Summary
The Protein Data Bank in Europe (PDBe) enhances macromolecular structure data with improved RNA mapping, cofactor identification, and advanced visualization tools. These updates facilitate easier access and interpretation for researchers using protein structure databases.
Area of Science:
- Structural biology
- Bioinformatics
- Biochemistry
Background:
- The Protein Data Bank in Europe (PDBe) is a key resource for macromolecular structure data.
- Effective data access, visualization, and analysis are crucial for diverse research communities.
Purpose of the Study:
- To detail data enrichment efforts at PDBe.
- To introduce new features for enhanced data access, visualization, and analysis of macromolecular structures.
Main Methods:
- Enrichment of Protein Data Bank (PDB) data, including mapping RNA structures to Rfam and identifying cofactors.
- Development of an advanced search facility with extensive data categories and sequence search capabilities.
- Integration of new features into the LiteMol viewer for improved visualization of carbohydrates and nucleic acids, and enhanced mapping of small molecules.
Main Results:
- Enhanced mapping of RNA structures to Rfam and identification of cofactor molecules.
- Implementation of a sophisticated search interface with numerous data categories.
- Upgraded visualization tools in LiteMol for better interpretation of complex molecular structures, including small molecules.
Conclusions:
- PDBe's data enrichment and tool development significantly improve the usability of macromolecular structure data.
- These advancements empower researchers to more readily find and interpret structural information, aiding scientific discovery.
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