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| Software | Best For | Limitations | |----------|----------|--------------| | | Visualization, basic docking | Less powerful docking than Glide | | PyMOL (open-source version) | High-quality molecular graphics | No built-in docking or dynamics | | AutoDock Vina | Molecular docking | Command-line only, steeper learning curve | | GROMACS | Molecular dynamics | No integrated GUI | | Open Babel | File format conversion | Limited analysis tools |