Open3DALIGN is an open-source software aimed at unsupervised molecular alignment.
Open3DALIGN 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.
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:
- A dataset is imported as SDF file
- 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
- 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
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
- Finally, an SDF database
constituted by the dataset compounds aligned to each of the templates is obtained
The QMD search is accomplished running a number of short molecular dynamics runs
(using the MMFF94 force-field) followed by minimization
(using the MMFF94s force-field); these computations are carried out
by calling four programs belonging to the
molecular mechanics suite (namely,
optimize) included in Open3DALIGN.
MMFF94 atom types are automatically assigned to all compounds of the dataset
with the help of
another tool of ours based on
Alignments are computed in an atom-based fashion (by means of a novel algorithm
inspired to the LAMDA algorithm by Richmond and co-workers), in a
pharmacophore-based fashion using
as the alignment engine, or finally in a mixed mode consisting in the combination
of the latter two methods.
High computational performance is attained splitting the computational tasks
over several threads, according to the number of CPUs available in the host
All computations can be restarted from the point from which they were eventually
stopped, allowing most intensive alignment tasks to be completed also in the
presence of time-limited computational resources.
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 *NIX 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.
A detailed ChangeLog is kept
to keep track of the additions and modifications during Open3DALIGN's