| Extension | File Type Description |
|---|---|
| .al2 | Alchemy 2000 |
| .mol | Alchemy III |
| .ros | Beilstein Institute's ROSDAL |
| .csd | Cambridge Crystallographic |
| .fdat | Cambridge Crystallographic |
| .dat | Cambridge Crystallographic |
| .cpd | Catalyst |
| .chm | Catalyst Query |
| .msi | Cerius2 |
| .cxf | Chemical eXchange Format |
| .cif | Crystallographic Information File |
| .hin | HyperChem |
| .car | InsightII CAR |
| .grd | InsightII Grid |
| .jdx | JCAMP-DX |
| .chm | ChemDraw |
| .cdt | ChemDraw Connection Table |
| .str | Kekule STR |
| .kin | Kinemage |
| .mol | MDL MOL |
| .sdf | MDL SD |
| .skc | MDL ISIS SKC |
| .tgf | MDL ISIS TGF |
| .mpg | Molecular Presentation Graphics |
| .nc | network Common Data Form |
| .pcm | PCModel |
| .pir | PIR/NBRF PIR |
| .ent | Protein Databank |
| .pdb | Protein Data Bank |
| .msf | Quanta |
| .seq | Scivision SEQ |
| .smi | SMILES |
| .scf | Softshell SCF |
| .sw | SWISSPROT/GCG |
| .tsw | SWISSPROT/GCT |
| .ml2 | Sybyl MOL2 |
| .mol2 | Sybyl MOL2 |
| .sy2 | Sybyl MOL2 |
| .sln | Tripos Sybyl line notation |
| .chp | Tripos ChemPrint |
| .hit | UNITY Hitlist format |
| .msv | WebLab Viewer |
| .wvc | Viewer Script |
| .log | Viewer Script |
| .xra | X-Ray Cartesian Coordinate data |
| .xyz | XYZ Coordinate |