Advanced PDB search

Advanced PDB search provides query-based access to Protein Data Bank (PDB) 3D structural data to support structural biology, structure-based drug design, genetic variation mapping, and integration with EMPIAR and EMBL-EBI resources.

Key Features:

• Extensive Data Access: Provides access to the 3D structural data stored in the Protein Data Bank (PDB).
• Interoperability: Integrates with EMBL-EBI resources, including the European Variation Archive and EMPIAR for electron microscopy data.
• Scalable Infrastructure: Operates on EMBL-EBI infrastructure with increased disk capacity (75 petabytes as of December 2015) to support large-scale queries.
• Resource Description Framework (RDF): Uses RDF to enable data integration and facilitate complex queries across diverse biological datasets.
• Embassy Cloud Integration: Integrates with EMBL-EBI's Embassy Cloud to enable computational analyses in a virtual environment using EMBL-EBI public data resources.

Scientific Applications:

• Structural Biology Research: Supports detailed analysis of protein structures to investigate molecular functions and interactions.
• Drug Discovery: Supports structure-based drug design by identifying potential binding sites and modeling ligand interactions.
• Genetic Variation Studies: Complements the European Variation Archive to assess structural implications of genetic variants.
• Electron Microscopy Data Analysis: Works with EMPIAR to analyze macromolecular complexes from electron microscopy data.

Methodology:

Implements algorithms for data retrieval and analysis, supports complex queries that integrate PDB structural data with other biological information, and employs RDF alongside EMBL-EBI cloud computing resources for processing.