Open3DALIGN

Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. The usual workflow is: 1) a dataset is imported as SDF file; 2) for each compound of the dataset a quenched molecular dynamics (QMD) conformational search is carried out to find the most stable conformers in a user-defined energy range from the global minimum; 3) a number of template compounds are chosen with different criteria, and the whole dataset is best-aligned to the template compounds. Since each compound is actually a collection conformers, the whole dataset is best-aligned (i.e., the best-fitting conformer is aligned) to every conformer of the template. This gives rise to a number of datasets which are aligned to a certain template conformer. The QMD search is accomplished running a number of short molecular dynamics runs (using the MMFF94 force-field) followed by minimization (using the MMFF94s force-field); these computations are carried out by calling two programs belonging to the TINKER molecular mechanics suite included in Open3DALIGN. MMFF94 atom types are automatically assigned to all compounds of the dataset by Open3DALIGN with the help of OpenBabel. Open3DALIGN sorts out diverse conformations in a user-specified range from the global minimum and saves them in SDF databases for later use. Once these conformational databases have been obtained, Open3DALIGN allows to find the best alignments to user-selected templates choosing the best-fitting conformers out of the available conformational pool. Alignments are computed using Pharao as a pharmacophore-based alignment engine. High computational performance is attained splitting the computational tasks over several threads, according to the number of CPUs available in the host running Open3DALIGN. Open3DALIGN 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 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 Open3DALIGN's development.