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arXiv · 2606.24487

CABS-flex standalone 3: an open command-line platform for protein flexibility simulation, peptide structure modeling, and protein-peptide docking

Chandran Nithin·Karol Wroblewski·Piotr Szukalo·Ayomide Fasemire·Aleksander Kuriata·Mateusz Kurcinski·Andrzej Kolinski·Sebastian Kmiecik
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Abstract

Summary: CABS-flex standalone 3 is an open command-line platform for fast CABS-based coarse-grained modeling of protein flexibility, peptide structures, and global or information-guided protein-peptide docking, coupled with all-atom reconstruction and analysis. The package builds on the established CABS-flex and CABS-dock ecosystem, widely used in structural bioinformatics for protein flexibility simulations and flexible protein-peptide docking. It provides a Python 3 implementation that brings together previous standalone functionality with recent developments in protein flexibility simulation, linear and cyclic peptide modeling, extended reporting and visualization, and deep-learning-based all-atom reconstruction with cg2all. Availability and Implementation: CABS-flex standalone 3 is implemented in Python 3 and is freely available as an open-source command-line package. Documentation is available at https://cabsflex.lcbio.pl. Source code is available at https://github.com/LCBio/CABSflex_standalone.

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Chandran Nithin, Karol Wroblewski, Piotr Szukalo, Ayomide Fasemire, Aleksander Kuriata, Mateusz Kurcinski, Andrzej Kolinski, Sebastian Kmiecik. 2026-06-23. CABS-flex standalone 3: an open command-line platform for protein flexibility simulation, peptide structure modeling, and protein-peptide docking. https://arxiv.org/abs/2606.24487

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