Open3DQSAR is an open-source
tool aimed at pharmacophore exploration by high-throughput chemometric
analysis of molecular interaction fields (MIFs).
Open3DQSAR can generate steric potential, electron density and
MM/QM electrostatic potential fields; furthermore, it can import
GRIDKONT binary files produced by
CoMFA/CoMSIA fields (exported from
with the aid of a small SPL script),
grid interaction fields (exported from
with the aid of a small SVL script).
Subsequently, Open3DQSAR performs fast, automated PLS chemometric
analysis of MIFs allowing to quickly generate and challenge the
predictivity of many 3D-QSAR models using different training/test
set combinations, superposition schemes, variable selection and
data scrambling procedures, etc. High computational performance is
attained through implementation of parallelized algorithms for MIF
generation, PLS model building and validation, variable selection.
- Multi-threaded computation of MIFs (both MM and QM); support
for the MMFF94 force-field with automated assignment of atom
types to the imported molecular structures
- Comprehensive output, including SDF molecular databases,
3D maps and many different plots to ease immediate evaluation of
results in PyMOL,
- Interface to
to compute local COSMO σ-profile (LSP)-based MIFs from within Open3DQSAR
Open3DQSAR is controlled through a command line interface; commands can be either
entered interactively from a command prompt or read from a batch script.
is installed on the system while Open3DQSAR is being operated
interactively, the setup of 3D grid computations can be followed
in real time on PyMOL's viewport, allowing to tweak grid size and
training/test set composition very easily
(take a look at the
gallery for some examples).
The main output is arranged as human-readable plain ASCII text, while
a number of additional files are generated to store data and to export
the results of computations for further analysis and visualization with
third party tools. In particular, Open3DQSAR can export 3D maps for
and can generate graphical statistic output ready to be imported into
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 Open3DQSAR's