Name Usage
Schrodinger Suite Molecular modeling and chemoinformatics
OpenEye Suite Molecular modeling
ChemAxon Suite Chemoinformatics
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 Graphing software
GNUPLOT Graphing software
PyMol Molecular visualization system
VMD Molecular visualization system​
RasMol ​Molecular visualization system
BLAST Sequence analysis
Clustal Omega Multiple sequence alignment
EMBOSS Bioinformatics analysis


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