AFM-Assembly is a suite of scripts and programs for assembling three-dimensional structures (PDB format) under the experimental constraint of the topographic surface of a molecule of interest.
AFM-Assembly bridges the gap between high-resolution AFM imaging of single, isolated particles and three-dimensional molecule assembly at the atomic level.
Admittedly, the resolution of an AFM topographic surface is not sufficient to directly constrain the positioning of atoms/residues from a topographic surface. However, it is entirely possible to assemble different pieces of a structure, or complex, from PDB files, all under the experimental constraint of single molecules.
The big difference between AFM imaging and electron microscopy is the unique signal-to-noise ratio of an AFM topography, which allows us to “see” the global conformation of a single molecule (with a practical resolution of nm).
AFM-Assembly was originally developed by Minh-hieu Trinh and extended in its current form by Rui M. Chaves for fitting and assembly.