Ofac

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Overlap Factor - often abbreviated OFAC is a measure of the steric clash between two atoms.

It is defined as ?distance between atom centers/(sum covalent radii)?.

Many of the PLOP algorithms rely on the rapid identification of steric clashes to eliminate conformations as being unreasonable before wasting time on calculating an energy (which would be huge). PLOP also reports steric clashes at various stages, including when loading a PDB structure. As a result, there is a need for a clear, simple-to-compute definition of a steric clash. The definition we use is the "overlap factor", which is defined as the ratio of the distance between two atom centers to the sum of their van der Waals radii. This definition has the advantage that it is independent of the atom types in question. This number will be less than 1 if the two atom spheres interpenetrate at all. Some interpenetration is normal, for example in a hydrogen bonding arrangement, and does not lead to a huge Lennard-Jones energy. Overlap factors of 0.8 or even 0.75 are common in high resolution x-ray crystal structures. An overlap factor of 0.7 would be a relatively minor steric clash, while 0.65 or lower would be more severe. Many of the prediction algorithms allow the specification of the overlap factor used to screen out conformations; there are default values set, but you may wish to override them in specific cases. For example, if performing optimizations on an initial structure with many steric clashes, it may be necessary to use a lower overlap factor to successfully generate any new (side chain/loop/helix) conformations at all.

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