[2][3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein.
The program also incorporates limited functions for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous proteins and thus difficult to predict by homology modeling.
Modeller was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco.
[4] It runs on the operating systems Unix, Linux, macOS, and Windows.
Graphical user interfaces (GUIs) and commercial versions are distributed by Accelrys.