Taking a Numeric Path. Idan Szpektor. The Input. A partial description of a molecule: The atoms The bonds The bonds lengths and angles Spatial constraints on some of the atoms of a molecule. The Questions. Is there a conformation of the molecule that answers the spatial constraints?
Torsion angles are (usually) unconstrained
a large number of degrees of freedom
The answers to the questions are not easy to find analytically. They are also resource consuming (running time).
S. M. Lavalle, P. W. Finn, L. E. Kavraki, J. C. Latombe (2000)
The coordinate frame of the molecule could be rotated with respect to the global coordinate frame of the pharmacophore feature positions
Another global coordinate frame transformation is needed
A. A. Canutescu and R. L. Dunbrack Jr. (2003)