We appreciate keeping the following citations in mind when using the BioAFMviewer:

Software paper

Amyot R, Flechsig H (2020) BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics. PLoS Comput Biol 16(11): e1008444.

Automatized fitting to AFM images

Amyot R, Marchesi A, Franz CM, Casuso I, Flechsig H (2022) Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. PLoS Comput Biol 18(3): e1009970.

Review paper

Amyot R, Kodera N, Flechsig H (2023) BioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamics. Journal of Structural Biology: X, 100086.

Sample-surface electrostatics

Amyot R, Nakamoto K, Kodera N, Flechsig H (2023) Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions. Frontiers in Molecular Biosciences 10.

GPU-accelerated calculations

Amyot R, Kodera N, Flechsig H (2024) Atom filtering algorithm and GPU-accelerated calculation of simulation atomic force microscopy images. Algorithms 17.1.