Comparison of xBFreE vs other programs¶
This comparison is based on the documentation of the different programs
Calculation features¶
| Feature | xBFreE | gmx_MMPBSA | MMPBSA.py | g_mmpbsa | CaFe |
|---|---|---|---|---|---|
| Binding free energies | PB and GB | PB and GB | PB and GB | PB | PB |
| * PB models | Linear and Non-Linear | Linear and Non-Linear | Linear and Non-Linear1 | Linear and Non-Linear | Linear and Non-Linear |
| * GB models | 1, 2, 5, 7, 8 and NSR6 | 1, 2, 5, 7, 8 and NSR6 | 1, 2, 5, 7 and 8 | ||
| Stability | |||||
| Alanine scanning | 2 | ||||
| Entropy corrections 3 | NMODE, QH, IE, and C2 | NMODE, QH, IE, and C2 | NMODE and QH | ||
| Decomposition schemes | Per-Residues and Per-Wise | Per-Residues and Per-Wise | Per-Residues and Per-Wise | Per-Residues | |
| QM/MMGBSA | |||||
| MM/3D-RISM | |||||
| Support Membrane Protein | |||||
| Approximations | ST and MT | ST and MT | ST and MT | ST | ST |
Technical features¶
| Feature | xBFreE | gmx_MMPBSA | MMPBSA.py | g_mmpbsa | CaFe |
|---|---|---|---|---|---|
| MD Program | GROMACS, AMBER, NAMD, CHARMM 7 | GROMACS | AMBER | GROMACS | NAMD, AMBER |
| * GROMACS Version | 5.x and 20xx.x | 4.x, 5.x and 20xx.x | --- | 4.x, 5.x and 2016+ 6 | |
| Dependencies | AmberTools >=20 and Delphi | AmberTools >=20 | AmberTools | APBS (1.2.x, 1.3.x or 1.4.x) | VMD, APBS or Delphi |
| Parallel computation | Depends on APBS | ||||
| Steps for: | |||||
| * Calculation and Summary | One | One | One | Multiple | One |
| * Analysis | One | One | Multiple | Multiple | Multiple |
Analysis features¶
Please, check the xBFreE-Analyzer documentation for more information.
| Feature | xBFreE | gmx_MMPBSA | MMPBSA.py | g_mmpbsa | CaFe |
|---|---|---|---|---|---|
| API | |||||
| Analyzer Tool | 4 | ||||
| * Multiple systems at same time | |||||
| * Correlation between systems | |||||
| * Per-residue energies to PDB | |||||
| * Interactive visualization | |||||
| ** 3D Molecular Visualization | PyMOL | PyMOL | |||
| ** Interactive Charts | static image | ||||
| * Plotting tool | xBFreE-Analyzer | gmx_MMPBSA_ana | API and graphics library 5 | internal tools | |
| * Energetic Terms charts | All | All | ΔGpolar, ΔGnonpolar, ΔEMM and ΔGbind | ||
| * Export data to CSV file | |||||
| ** Energy Summary | |||||
| ** Individual Energetic Terms |
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Requires the user to modify manually the *.mdin input files ↩
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Without documentation ↩
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NMODE = Normal modes approximation, QH = Quasic-Harmony approximation, IE = Interaction Entropy approximation, and C2 = C2 Entropy ↩
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We plan to extend xBFreE-Analyzer compatibility to MMPBSA.py's results ↩
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Currently there is a repository (AmberUtils) for analysing the results ↩
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GROMACS 20xx.x is not officially supported. There is a Pull Request that offers a minimum compatibility with versions higher than 2016.x one, but still with limitations ↩
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xBFreE currently supports a variety of topology/trajectory formats including but not limited to: *.top, *.prmtop, *.psf, and *.xtc, *.mdcrd, *.dcd. These formats can be used by other MD engines, and hence they are supported in xBFreE as well. ↩