Genevieve Evans
AlphaFold DB Bioinformatician,
Protein Databank in Europe
HT4: Databases
T1 (Tutorial): Access, Visualisation & Evaluation at PDBe & PDBe-KB
PART I:
The PDB archive is a freely-available database that predates the internet and reflects a generous spirit and foresight from the structural biology community. Analysis of this database has often yielded new insights, and these insights have driven the development of new tools and improvements to the process of determining new structures.
This hands-on session will focus on how to find an interesting data cohort for comparison / analysis using PDBe search tools and the PDBe webpages.
Learning outcomes
- How to download a sets of coordinate files
- Tools for navigating coordinate files in mmCIF file format
- Search the PDB for different cohorts of data
- Step towards programmatic access
– introduction to Solr-based queries
PART II:
PDBe-KB is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive from the bioinformatic community. PDBe-KB is a flagship of the ELIXIR 3D-BioInfo Community (elixir-europe.org/communities/3d-bioinfo), an international group of researchers and software developers working on improving use of macromolecular structure data in life science research.
Learning outcomes
- Become aware of pre-populated analysis
& information provided via PDBe-KB- Visualise and analyse sets of structures, pre-grouped
- Structural superposition data, pre-determined
- Sequence-based knowledge mapped onto a sets of structures
- Integrating PDBe-KB with alternative search approaches:
- g. fold-centric search
