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, CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script), and MOE grid interaction fields (exported from and MOE with the aid of a small SVL script).

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

Most prominent features in Open3DGRID include:

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.