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.

If you use the Normal Mode Flexible Fitting AFM (NMFF-AFM) method, please cite the two following papers:

Wu X, Miyashita O, Tama F (2024) Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis. The Journal of Physical Chemistry B, 128(39), 9363-9372.

Amyot R, Miyashita O, Wu X, Takeda K, Kodera N, Konno H, Tama F, Flechsig H (2025) Flexible fitting to infer atomistic-precision models of large-amplitude conformational dynamics in biomolecules from high-speed atomic force microscopy imaging. bioRxiv.