A new method for the automatic determination of cores in proteins

An algorithm is described for automatically detecting cores in proteins of known structure. A core is identified as a tightly packed part of the protein, consisting of solvent-inaccessible atoms. Unlike other methods, here the search for a core is not limited only to nonpolar contacts and elements of secondary structure. The proposed algorithm is simple and fast. Data obtained with the help of the method are in reasonable agreement with experimental results.