Software
NAFlex is powered by an Apache 2. web server with PHP 5. and MySQL 5.0.51. Calculations are redirected to a 8 core Intel(R) Xeon(R) CPU @ 2.67GHz - 16GB RAM cluster managed by a Sun Grid Engine batch manager.
List of external software used in NAFlex operations:
| Program | Description | Package & Version |
| Curves+, Canal | Analysis of Nucleic Acids Structure and Flexibility | Curves+ 2.0 |
| Open Babel | Chemical toolbox designed to work with many languages of chemical data. | Open Babel 2.1.1 |
| R Statistics | Statistical Computing and Graphics software. | R 2.15.0 |
| BLAST | Basic Local Alignment Search Tool | BLAST 2.2.17 |
| CMIP | Classical Molecular Interaction Potential | CMIP 2.5.4 |
| Gnuplot | Plotting tool | Gnuplot 4.2 patchlevel 2 |
| Grace | Plotting tool | Grace 5.1.21 |
| GROMACS | Molecular Dynamics Simulator | GROMACS 4.5.5 |
| JMol | Molecular Graphics Viewer | JMol 10.00.46 |
| MobyLite PerlAPI | BioMoby Perl API | MobyLite PerlAPI 1.0 |
| NAMD | Molecular Dynamics Simulator | NAMD 2.8 |
| PCAsuite | Trajectory compression tool | PCASuite 1.1 |
| PropKa | Prediction of protein pKa values | Propka 2.0 |
| Ptraj, cpptraj | Structure and dynamic analysis of trajectories | Ambertools 14 |
| tgatoppm, pnmcrop, pnmtopng | Image management | Netpbm 10.0 |
| Tleap | MD preparation program | Ambertools 14 |
| VMD | Molecular Graphics Viewer | VMD 1.8.5 |
