We have developed a new version of PISA, which focuses on analysing intermolecular interactions within existing assemblies. This updated version, named PISA-lite, generates new and enhanced PISA interaction data based on all the annotated assemblies in the PDB archive and is available in JSON format from the PDBe API. This work has been done in collaboration with the core team.
PISA-lite
We are excited to announce the release of the new version of the Proteins, Interfaces, Structures and Assemblies (PISA) software, developed at PDBe, based on the jsPISA implementation from CCP4. This new version, called PISA-lite, enables the calculation of macromolecular interaction data for every assembly in the PDB.
PISA-lite is a new addition to the PDBe weekly release process. It generates interaction data in JSON format, loaded into the PDBe graph database, and made available through new PDBe API endpoints and JSON files in the PDBe FTP area. PISA-lite is designed to reduce the computational overhead of the software by working only on known assemblies in PDB entries and calculating interactions.
By focusing on known assemblies, PISA-lite enables the weekly calculation of macromolecular interactions for each assembly in the PDB, providing up-to-date information on protein structures and their interactions. Providing these pre-calculated annotations makes PISA-lite an essential tool for researchers in structural biology, bioinformatics, and related fields.
PISA-lite will benefit the scientific community by providing easy access to up-to-date macromolecular interactions data. We invite users to try out this new version of the PISA software and provide us with feedback on their experience.
Access to PISA-lite data
The data generated by PISA-lite has been expanded to include more information on individual interfaces, including more types of atom-atom interactions.
On 30 Mar 2023, the legacy PISA API endpoints will be retired and replaced with three new API endpoints, which return responses in JSON format. The data are obtained from PISA-lite and contain detailed information about protein interfaces and macromolecular assemblies for each entry in the PDB.
The details for a given assembly in the PDB are provided in JSON format through the following API endpoint:
/pdbe/api/pisa/assembly/:pdbid/:assemblyid
The JSON response includes the following details of the requested assembly:
- Size of the assembly
- Dissociation energy
- Accessible surface area
- Entropy
- Dissociation area
- Solvation energy gain
- Formula
- Composition
The interface details for a given assembly in the PDB are provided in JSON format through two API endpoints specific to a single interface or for all interfaces in the assembly:
/pdbe/api/pisa/interface/:pdbid/:assemblyid/:interfaceid
/pdbe/api/pisa/interface/:pdbid/:assemblyid
The JSON response keyed on an assembly identifier includes new data and information for interfaces and assemblies:
- Details of the assembly (as above)
- List of valid interfaces of protein complexes (polymer-polymer interactions)
- List of van der Waals contacts (with a cutoff of 4 Angstroms, labelled as 'other bonds')
- Atom-atom interaction details for each contact:
- Residue names (Three-letter code)
- Author chain identifier
- Interface UniProt accession numbers
- Sequence position of the UniProt entry that corresponds to the residue mapping where available
- Author atom sequence identifiers
- Asym chain identifiers in the original model
- Sequence number (label)
- Atom insertion code
The JSON schemas of these endpoints are available on . All the pre-calculated data are also available as JSON-formatted files from the and are loaded into the PDBe graph database.
