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. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.
A typical workflow could be the following:
1. A dataset is imported as SDF file
2. Optionally, 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. One or more template compounds are chosen, then the whole dataset is best-aligned to the template(s). The alignment is a performed rigidly, using for each compound of the dataset either the single conformation originally imported or the conformational databases previously obtained by QMD. Additionally, SDF conformational databases can be easily imported from external conformational engines such as MOE and OMEGA. In the latter case, the conformers which best fit the template(s) are chosen out of the conformational pool. Interestingly, conformational flexibility may also be taken into account for templates.
4. Finally, an SDF database constituted by the dataset compounds aligned to each of the templates is obtained
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 four programs belonging to the TINKER molecular mechanics suite (namely, analyze, dynamic, minimize and optimize) included in Open3DALIGN. MMFF94 atom types are automatically assigned to all compounds of the dataset with the help of SDF2XYZ2SDF, another tool of ours based on OpenBabel.
Alignments are computed in an atom-based fashion (by means of a novel algorithm inspired to the LAMDA algorithm by Richmond and co-workers), in a pharmacophore-based fashion using Pharao as the alignment engine, or finally in a mixed mode consisting in the combination of the latter two methods.
High computational performance is attained splitting the computational tasks over several threads, according to the number of CPUs available in the host running Open3DALIGN.
All computations can be restarted from the point from which they were eventually stopped, allowing most intensive alignment tasks to be completed also in the presence of time-limited computational resources.
Thyroid hormones play an essential role for metabolism, growth and differentiation. Therefore, exact regulation of thyroid hormone levels is vital for most organisms. Although the principles of thyrotropic feedback ... thyrotropic feedback. SimThyr is a simulation program for the pituitary thyroid feedback control that is based ... base of a BSD licence. Binaries are available for Mac OS, Mac OS X and Windows, sourcecode .... Free download of SimThyr for Mac OS X 22.214.171.1242
FreeMedForms is free and open source software, available for all current platforms (Linux, Mac OS X, Windows and FreeBSD). It is powerful and fully ... file that you can modify to suit best for your practice. You can also customize your main ... can set your personal agenda. Create an appointment for one or more patients in a single click .... Free download of FreeMedForms for Mac OS X 0.9.0
... performance is attained through implementation of parallelized algorithms for MIF generation, PLS model building and validation, variable ... 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 .... Free download of Open3DQSAR for Mac OS X 2.24
... or plot data, analyze data and prepare it for printing. This software is special because it combines ... · Save, print, export your results (for example for scientific publications, homework) .... Free download of QtGrace for Mac OS X 0.2.3 Beta
... across a landscape simultaneously. We are developing Circuitscape for Mac OS X, Windows, and Linux. .... Free download of Circuitscape for Mac OS X 3.5.8
Developed to be a simulation & development environment. Free download of VirtualBreadboard 5.42
A comprehensive astronomical manager and photo editor. Free download of MaxIm DL 5.24
Home design software for PCs with XP or Vista or Windows 7, 8, 10. Free download of Ez-Architect 8.0
Embird Embroidery Software - Software for Computerized Embroidery and Quilting.. Free download of Embird 2012