In this paper, a 3D structure-based approach is presented for the efficient classification of protein molecules. The method relies on the geometric 3D structure of the proteins. After proper positioning of the 3D structures, the Spherical Trace Transform is applied to them to produce geometry -based descriptors, which are completely rotation invariant. Additionally, some biological properties of the protein are taken, and added to the geometry-based descriptor, thus forming better integrated descriptor. We have used nearest neighbour classification on the previously extracted descriptors. A part of the FSSP/DALI database, was used to evaluate the classification accuracy of this system. The results show that this method achieves more than 92 percent classification accuracy while it is simpler and faster than the DALI method. We provide some experimental results of the implemented system.