by Hamish Carr (BETA-Lab / Theory Group)
One of the principal tasks in protein chemistry is to determine the 3-dimensional shape of a protein, given that the chemical sequence is known. One of the principal methods of determining shape involves crystallizing the protein, constructing an electron density map in three dimensions, and analyzing this map. This is often done by hand, but can also be automated: molecular scene analysis is one of the names applied to the automated approach.
One property of the electron density map that is useful is that peaks (local maxima) occur at atoms, and passes (saddle points) occur at chemical bonds. Extracting the critical point graph is, therefore, a common step in molecular scene analysis.
I shall describe the critical point graph, the standard method for extracting it (ORCRIT), and a proposed alternative method based on topological tools.
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