Term information
Algorithm for the calculation of the occluded surface. "Occluded surface is defined as the molecular surface that is less than 2.8 Angstroms from the surface of neighboring non-bonded atoms. That is, if a water molecule cannot fit between two atoms they occlude each other. Occluded surface is similar to buried surface but is more sensitive to packing geometry than buried surface using a rolling probe. To calculate occluded surface, normals at the molecular surface are extended outward until they intersect neighboring van der Waals surface. The collection of extended normals, and their respective lengths, defines the packing of each atom in a structural model. The figure above illustrates this concept. Analysis of the occluded surface enables one to identify amino acid residues in unusual occluded surface environments compared to a database of high resolution structures. Residues in an unusual environment are frequently incorrectly modeled, involved in crystal contacts, or involved in ligand binding. " http://www.csb.yale.edu/userguides/datamanip/os/