is a command-line utility which allows you to compare the 3D structure of proteins. The input files (PDB format) can be any two Brookhaven files. 3DPAln enables you to perform the analysis of subunit contents in both files, and select the alignment for any two subunits from all the subunits contained in both files.
The program does not require any sequence gomology or any previous assumption about 3D structure similarities of starting proteins. It can automatically determine the degree of 3D similarity.
The output consists of the 3D coordinates of the second subunit rotated and shifted for a best fit with the coordinates of the first subunit.
You can display and manipulate the stereoscopic image of the starting structures and the final results for both proteins using mirror stereo-glasses.
In addition, 3DPAln allows you to generate a second type of output: a linear representation of the 3D alignment, as well as a listing of the conservative regions of the structure which fit with the given Root Mean Square (RMS) deviations.
Please note that the program also runs in Windows 3.1.