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 GRID and CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL 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.
FEATURES:
· Multi-threaded computation of MIFs (both MM and QM); support for MMFF94 and GAFF force-fields 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, MOE, Maestro, SYBYL and gnuplot
· User-friendly interface to all major QM packages (e.g. GAUSSIAN, FIREFLY, GAMESS-US, MOLDEN) allows calculation of QM electron density and electrostatic potential 3D maps from within Open3DQSAR
· User-friendly interface to Molecular Discovery GRID to compute GRID MIFs from within Open3DQSAR
