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
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
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
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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