TransAtlas:
Atlas of Protein Conformational Transitions
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TransAtlas Software
TransAtlas is powered by an Apache 2 web server with PHP 5.2.4 and MySQL 5.0.51.
List of software / tools / packages used in TransAtlas:
| Program | Description | Package & Version |
| R Statistics | Statistical Computing and Graphics software | R 2.15.0 |
| GROMACS | Molecular Dynamics Simulator | GROMACS 4.5.5 |
| JSMol | Molecular Graphics Viewer | JMol 14.0.5 (HTML5) |
| Ptraj, cpptraj | Structure and dynamic analysis of trajectories | Ambertools 14 |
| Grace | Plotting tool | Grace 5.1.21 |
| VMD | Molecular Graphics Viewer | VMD 1.8.5 |
| Plumed | Free energy calculations in molecular systems | Plumed 2.2 |
| GOdMD | Coarse-Grained Molecular Dynamics Simulator | GOdMD v1.0 |
| Modeller | Comparative Protein Structure Modelling | Modeller 9.15 |
| MDWeb | Molecular Dynamics on Web | MDWeb v1.0 |
| MMB PDB Mirror API | MMB Protein Data Bank (PDB) API | MMB PDB Mirror API |
| jsTree | jsTree jQuery tree plugin | jsTree v3.3.1 |