viAFM - a Python toolset for virtual Atomic Force Microscopy

10 September 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Atomic Force Microscopy (AFM) is a powerful but demanding imaging technique used also to study the interaction strength of single biomolecules by force spectroscopy. Here we provide a viAFM program designed to facilitate multi- directional steered molecular dynamics simulations and analysis of forces required to disrupt protein complexes thus mimicking AFM force spectroscopy experiments. Our viAFM tool allows for rapid assessment of protein-protein interaction strength, anisotropy, and the impact of ligands or mutations on complex stability, enabling efficient testing of drug candidates.

Keywords

Atomic force microscopy
molecular dynamics
protein protein interactions
protein ligand interactions

Supplementary materials

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viAFM supplementary information
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viAFM supplementary information
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Supplementary weblinks

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