Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images

B Dasgupta, O Miyashita, F Tama - Biochimica et Biophysica Acta (BBA) …, 2020 - Elsevier
Abstract Background Atomic Force Microscopy (AFM) is an experimental technique to study
structure-function relationship of biomolecules. AFM provides images of biomolecules at …

Flexible fitting of biomolecular structures to atomic force microscopy images via biased molecular simulations

T Niina, S Fuchigami, S Takada - Journal of Chemical Theory and …, 2020 - ACS Publications
High-speed (HS) atomic force microscopy (AFM) is a prominent imaging technology that
observes large-scale structural dynamics of biomolecules near the physiological condition …

Protein dynamics by the combination of high-speed AFM and computational modeling

H Flechsig, T Ando - Current Opinion in Structural Biology, 2023 - Elsevier
High-speed atomic force microscopy (HS-AFM) allows direct observation of biological
molecules in dynamic action. However, HS-AFM has no atomic resolution. This article …

[HTML][HTML] Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images

R Amyot, A Marchesi, CM Franz, I Casuso… - PLoS computational …, 2022 - journals.plos.org
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under
near-physiological conditions. However, the scanning tip probes only the molecular surface …

[HTML][HTML] Case report: Bayesian statistical inference of experimental parameters via biomolecular simulations: atomic force microscopy

S Fuchigami, T Niina, S Takada - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
The atomic force microscopy (AFM) is a powerful tool for imaging structures of molecules
bound on surfaces. To gain high-resolution structural information, one often superimposes …

[HTML][HTML] BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

R Amyot, H Flechsig - PLoS computational biology, 2020 - journals.plos.org
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular
structures into the graphical representation corresponding to the outcome of atomic force …

Imaging proteins with atomic force microscopy: an overview.

LP Silva - Current protein & peptide science, 2005 - europepmc.org
Atomic force microscopy (AFM) has become a common tool for biophysical studies of
proteins; mainly due its property to perform characterizations near physiological conditions …

[HTML][HTML] Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

T Niina, Y Matsunaga, S Takada - PLOS Computational Biology, 2021 - journals.plos.org
Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological
condition, but the observed data are limited to the surface height of specimens. Since the …

[HTML][HTML] Computational reconstruction of multidomain proteins using atomic force microscopy data

MH Trinh, M Odorico, ME Pique, JM Teulon… - Structure, 2012 - cell.com
Classical structural biology techniques face a great challenge to determine the structure at
the atomic level of large and flexible macromolecules. We present a novel methodology that …

[HTML][HTML] Structural information, resolution, and noise in high-resolution atomic force microscopy topographs

P Fechner, T Boudier, S Mangenot, S Jaroslawski… - Biophysical …, 2009 - cell.com
AFM has developed into a powerful tool in structural biology, providing topographs of
proteins under close-to-native conditions and featuring an outstanding signal/noise ratio …