| Schrodinger Suite | Molecular modeling and cheminfortmatics |
| OpenEye Suite | Molecular modeling |
| ChemAxon Suite | Cheminformatics |
| Rosetta Suite | Molecular modeling and protein design |
| Autodock | Protein-small molecule docking |
| Dock6 | Protein-small molecule docking |
| GRAMM | Protein-protein docking |
| ChemOffice | Chemical productivity suite |
| OpenBabel | Chemical toolbox |
| CHARMM | Molecular dynamics |
| NAMD | Molecular dynamics |
| GROMACS | Molecular dynamics |
| LAMMPS | Molecular dynamics |
| NWChem | Quantum mechanics/molecular mechanics |
| GAMESS | Molecular quantum chemistry |
| R | Statistical computing and graphics |
| XMGrace | Graphic software |
| GNUPLOT | Graphic software |
| PyMol | Molecular visualization system |
| VMD | Molecular visualization system |
| RasMol | Molecular visualization system |
| BLAST | Sequence analysis |
| Clustal Omega | Multiple sequence alignment |
| EMBOSS | Bioinformatics analysis |