PSILO: A Protein Structure Database System

PSILO: A Protein Structure Database System


PSILO® is a database system that provides an easily accessible, consolidated repository for macromolecular and protein-ligand structural information. It offers research organizations a means to systematically track, register and search both experimental and computational macromolecular structural data. A web-browser interface facilitates the searching and accessing of public and private structural data.

Macromolecular Repository

  • Store and disseminate coordinate and structure factor data
  • Capture related working files, reports and other auxiliary files (all original data saved)
  • Generate standard PDB, mmCIF and XML format(fully compliant with RCSB standards)

Browser Interface for Search and Retrieval

  • Powerful and intuitive Google-like queries (with multiple search criteria)
  • Substructure and 3D queries use standard sketchers (ChemDraw®, etc.)
  • Download entire hit lists or individual records (PDB, mmCIF, XML, MDB) in crystal frame or predefined family reference frame
  • 2D and 3D active site visualization
PSILO - Search and Download Structures PSILO - 2D and 3D Visualization
Search and Download Structures 2D and 3D Visualization

3D Ligand:Receptor and Pocket Similarity Search

  • Ligand:receptor 3D geometry using standard sketchers
  • 3D pocket similarity search
  • 3D domain motif search
  • Combine with text search, 2D query information or other criteria
  • Automatic detection of ligand-independent pockets
PSILO - 3D Interaction Query PSILO - Pocket Similarity
3D Interaction Query Pocket Similarity

Analysis and Visualization

  • 3D query statistics: analyze interaction data, view scatter plots and histograms and sort by constraint values (distance, angle and dihedral)
  • BLAST search summary page with phylogenetic tree, interactive sequence alignment
  • Align structures by ligand, pocket, protein, family or 3D query, and visualize
  • Clickable 2D Ligand interaction diagrams linked to the 3D viewer
  • Visualize structures and weighted electron densities in 3D (or launch local viewer)

Data Standardization and Annotation

  • Automated standard orientations for related structures
  • Automatic mirroring of RCSB in weekly updates
  • Automatic bioinformatics annotations (GO, SCOP, antibody CDR, kinase domain, etc.)
  • Automatic geometric health checks to assess the quality of the data and protein quality summary
  • Web interface for individual record deposit
  • Bulk import script for larger datasets
PSILO - Bioinformatic Annotations PSILO - Real-space Correlation
Bioinformatic Annotations Real-space Correlation

Data Integration and IT Infrastructure

  • Standard IT Infrastructure, simple to maintain and deploy
  • Flexible integration with external/internal databases and software
  • Source code provided for customization
  • Group-based permission system


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