Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. It is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input.
If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.
A typical workflow could be the following:
1. A dataset is imported as SDF file
2. Optionally, for each compound of the dataset a quenched molecular dynamics (QMD) conformational search is carried out to find the most stable conformers in a user-defined energy range from the global minimum
3. One or more template compounds are chosen, then the whole dataset is best-aligned to the template(s). The alignment is a performed rigidly, using for each compound of the dataset either the single conformation originally imported or the conformational databases previously obtained by QMD. Additionally, SDF conformational databases can be easily imported from external conformational engines such as MOE and OMEGA. In the latter case, the conformers which best fit the template(s) are chosen out of the conformational pool. Interestingly, conformational flexibility may also be taken into account for templates
4. Finally, an SDF database constituted by the dataset compounds aligned to each of the templates is obtained

Usage
open3dalign [OPTION...]
-i <filein> Input is read from <filein>
-o <fileout> Output is written to <fileout>
-p Input is piped through standard input
-?, --help Give this help list
--usage Give a short usage message
-V, --version Print program version

The license of this software is Free, you can free download and free use this 3d graphic software.