3D Protein Alignment is an easy-to-use, command-line utility which allows you to compare protein alignment of 3D structures in PDB (Brookhaven) format for computer modelling purposes and protein structure classification. The program lets you determine the set of matched amino acids and the degree of 3D similarity between two proteins. The output consists of the 3D coordinates of the second protein, which are rotated and shifted to best fit the coordinates of the first protein. You can display and manipulate the stereo-image of the final results using the built-in mirror stereo-glasses function. In addition, the output includes a linear representation of the 3D alignment, and a list of the structurally conservative regions that correspond to the given RMS deviations.