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Open3DALIGN
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An open-source software aimed at unsupervised molecular alignment

Paolo Tosco (a,*), Thomas Balle (b)

a) Department of Drug Science and Technology,
   University of Turin, via Pietro Giuria 9, 10125 Torino, Italy;
   e-mail: paolo.tosco@unito.it

b) Department of Medicinal Chemistry,
   The Faculty of Pharmaceutical Sciences, University of Copenhagen,
   2 Universitetsparken, 2100 Copenhagen, Denmark

http://open3dalign.org




Open3DALIGN is a command-line tool aimed at unsupervised molecular
alignment.  The usual workflow is:

   1. a dataset is imported as SDF file
   2. 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 minimu
   3. a number of template compounds are chosen with different criteria,
      and the whole dataset is best-aligned to the template compounds.
      Since each compound is actually a collection of conformers, the whole
      dataset is best-aligned (i.e., the best-fitting conformer is aligned)
      to every conformer of the template. This gives rise to a number of
      datasets which are aligned to a certain template conformer.


The QMD search is accomplished by calling two programs belonging to the
TINKER molecular mechanics suite. Open3DALIGN sorts out diverse
conformations in a user-specified range from the global minimum and saves
them in SDF databases for later use. Once these conformational databases
have been obtained, Open3DALIGN finds the best alignments to user-selected
templates choosing the best-fitting conformers out of the available
conformational pool. Alignments are computed using Pharao as a
pharmacophore-based alignment engine.  High computational performance is
attained through multi-threaded algorithms.

Open3DALIGN is written in C; while pre-built binaries are available for
mainstream operating systems (Windows 32/64-bit, Linux 32/64-bit, Solaris
x86 32/64-bit, FreeBSD 32/64-bit, Intel Mac OS X 32/64-bit), source
code is portable and can be compiled under any platform supporting POSIX
threads. The modular nature of the code allows for easy implementation
of new features, so that the core application can be customized to meet
individual needs.