BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
PLoS Comput Biol
; 16(11): e1008444, 2020 11.
Article
in English
| MEDLINE | ID: covidwho-1040035
ABSTRACT
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Software
/
Microscopy, Atomic Force
Type of study:
Observational study
/
Prognostic study
Language:
English
Journal:
PLoS Comput Biol
Journal subject:
Biology
/
Medical Informatics
Year:
2020
Document Type:
Article
Affiliation country:
Journal.pcbi.1008444
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