Table 4.
List of software for MD simulation, Modeling, Docking, Visualization and analysis of Molecules.
| Reference | Description | Pros | Cons | Source code |
|---|---|---|---|---|
| AMBER [144] | A package for MD simulation | High Performance MD, Comprehensive trajectory analysis tools | License required for parallel CPU or GPU computation | https://ambermd.org/ |
| ACEMD [145] | An accelerated platform for faster and longer biomolecular simulations | Super computer level performance | License required for ful functionality | https://www.acellera.com/ |
| AutoDock Vina [146] | A program for molecular docking and screening | Receptor flexibility, blind docking | Difficult to dock small peptides | https://vina.scripps.edu/ |
| DeePMD [147] | A deep learning package for MD simulation and energy representation | Optimized code, interfaced with Tensorflow | Model compression issues | https://github.com/deepmodeling/deepmd-kit/ |
| RBio3D [148] | R package for the analysis of MD trajectories | Tools for protein-networks, conformations | - | http://thegrantlab.org/bio3d/ |
| Pymol [149] | An interactive platform for visualization of molecules | Homology Modeling, Docking, Virtual Screening | License required for full features | https://pymol.org/2/ |
| RosettaCommons [124] | A tool for predicting the mutant structure | Protein modeling and folding | Preference for aromatics, Preference for hydrogen bonding | https://www.rosettacommons.org/ |