PDBe PISA: Enhanced Analysis of Macromolecular Interactions

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Abstract
Protein interactions play a pivotal role in determining the biological functions of living cells. Gaining structural insights into protein interfaces can illuminate their role in function and diseases and highlight their potential as therapeutic targets. In response, there has been a marked increase in efforts by the scientific community to decipher the nuances of macromolecular interfaces, aiming to predict interactions and binding specificity of different components within complexes. The “Proteins, Interfaces, Structures, and Assemblies” (PISA) software has become a standard tool for analyzing intermolecular interactions and elucidating macromolecular assemblies from molecular structures. This article presents detailed protocols for using Protein Data Bank in Europe (PDBe) PISA API, a new Application Programming Interface (API) for enhanced analysis of protein assembly interfaces, using an updated version of PISA software. Compared to its predecessor, the updated PISA software expands interface data, increasing the coverage and detail of interaction information for assemblies and introduces greater computational flexibility, allowing users to perform targeted interface analyses for selected assemblies efficiently. The PDBe team uses the PISA API to provide interaction data in a JavaScript Object Notation (JSON) format for weekly Protein Data Bank (PDB) releases to support the efforts of the broader scientific community. Our protocols are a comprehensive guide to harnessing macromolecular interaction data using PISA. We delve into practical examples, from querying interaction and interface data from JSON files to extracting interaction data for assemblies cataloged in the PDB archive using programmatic access and bulk download via File Transfer Protocol (FTP). © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 : Programmatic access to interaction data with PDBe PISA API Basic Protocol 2 : FTP access to interaction data of assemblies Basic Protocol 3 : Analysis of assembly interfaces and interactions

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