This repository contains a script written in Java and based on the BioJava library to search for protein structures in the PDB that fulfill certain structural requirements.

The script was originally created to search for candidates for a fusion protein with two antiparallel terminal helices separated 11Å apart, in order to be able to solve its structure experimentally.

Clone the repository and install dependencies using Maven with mvn install.

Modify search criteria in the MotifParams class and run the MotifSearch script to start scanning PDB structures automatically. The list of PDB IDs matching the search criteria will be printed to the standard output.

If you found this repository useful for your work, please consider citing the following publication:

Cryo-EM structure of a single-chain β1–adrenoceptor – AmpC β-lactamase fusion protein
Gabriella Collu, Inayathulla Mohammed, Aleix Lafita, Tobias Bierig, Emiliya Poghosyan, Spencer Bliven, Roger M. Benoit
bioRxiv (2021); doi: https://doi.org/10.1101/2021.09.25.461805