TY - COMP

T1 - Open3DQSAR

T2 - An open-source software aimed at high-throughput chemometric analysis of molecular interaction fields

A2 - Tosco, Paolo

A2 - Balle, Thomas

N1 - Publication describing this software, CURIS id: 20196746

PY - 2011

Y1 - 2011

N2 - Description 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 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. Open3DQSAR features: •Seamless integration with OpenBabel, PyMOL, gnuplot •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, TURBOMOLE, 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 Open3DQSAR is controlled through a command line interface; commands can be either entered interactively from a command prompt or read from a batch script. If PyMOL 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 visualization in PyMOL, MOE, Maestro, SYBYL, and can generate graphical statistic output ready to be imported into gnuplot. Open3DQSAR 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 development.

AB - Description 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 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. Open3DQSAR features: •Seamless integration with OpenBabel, PyMOL, gnuplot •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, TURBOMOLE, 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 Open3DQSAR is controlled through a command line interface; commands can be either entered interactively from a command prompt or read from a batch script. If PyMOL 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 visualization in PyMOL, MOE, Maestro, SYBYL, and can generate graphical statistic output ready to be imported into gnuplot. Open3DQSAR 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 development.

KW - Former Faculty of Pharmaceutical Sciences

M3 - Computer programme

ER -