localpdb-a Python package to manage protein structures and their annotations

Motivation: The wealth of protein structures collected in the Protein Data Bank enabled large-scale studies of their function and evolution. Such studies, however, require the generation of customized datasets combining the structural data with miscellaneous accessory resources providing functional, taxonomic and other annotations. Unfortunately, the functionality of currently available tools for the creation of such datasets is limited and their usage frequently requires laborious surveying of various data sources and resolving inconsistencies between their versions. Results: To address this problem, we developed localpdb, a versatile Python library for the management of protein structures and their annotations. The library features a flexible plugin system enabling seamless unification of the structural data with diverse auxiliary resources, full version control and powerful functionality of creating highly customized datasets. The localpdb can be used in a wide range of bioinformatic tasks, in particular those involving large-scale protein structural analyses and machine learning.

Automated summary

This study developed localpdb, a versatile Python library for managing protein structures and annotations. It features a flexible plugin system for unifying structural data with diverse auxiliary resources, suitable for bioinformatic tasks, especially large-scale protein structural analysis and machine learning.