Open3DGRID: An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)

Research output: Non-textual formComputer programmeResearch

Paolo Tosco (Developer), Thomas Balle (Developer)

Description

Open3DGRID is an open-source software aimed at high-throughput generation of molecular interaction fields (MIFs). Open3DGRID 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).

High computational performance is attained through implementation of parallelized algorithms for MIF generation.

Most prominent features in Open3DGRID include:
•Seamless integration with OpenBabel, PyMOL, GAUSSIAN, FIREFLY, GAMESS-US, TURBOMOLE, MOLDEN, Molecular Discovery GRID
•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
•Human and machine-readable text output, integrated with 3D maps in several formats to allow visualization of results in PyMOL, MOE, Maestro and SYBYL
•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 Open3DGRID
•User-friendly interface to Molecular Discovery GRID to compute GRID MIFs from within Open3DGRID

Open3DGRID 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 Open3DGRID 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.
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, Open3DGRID can export 3D maps for visualization in PyMOL, MOE, Maestro and SYBYL.

Open3DGRID 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 Open3DGRID's development.
Original languageEnglish
Publication date2011
Publication statusPublished - 2011

ID: 34403085