Index by File Extension
- .alc - Alchemy format
- .bgf - MSI BGF format
- .box - Dock 3.5 Box format
- .bs - Ball and Stick format
- .c3d1 - Chem3D Cartesian 1 format
- .c3d2 - Chem3D Cartesian 2 format
- .caccrt - Cacao Cartesian format
- .car - Accelrys/MSI Biosym/Insight II CAR format
- .ccc - CCC format
- .cds - CD Style Sheet
- .cdx - ChemDraw format
- .cdxml - ChemDraw XML format
- .chm - ChemDraw 3.x format
- .cml - Chemical Markup Language
- .cmlr - CML Reaction format
- .crk2d - Chemical Resource Kit diagram format (2D)
- .crk3d - Chemical Resource Kit 3D format
- .ct - ChemDraw Connection Table format
- .dmol - DMol3 coordinates format
- .ent - Protein Data Bank format
- .feat - Feature format
- .fract - Free Form Fractional format
- .fs - FastSearching
- .g03 - Gaussian98/03 Output
- .g98 - Gaussian98/03 Output
- .gam - GAMESS Output
- .gamout - GAMESS Output
- .gpr - Ghemical format
- .hin - HyperChem HIN format
- .ins - ShelX format
- .jout - Jaguar output format
- .mdl - MDL MOL format
- .mmd - MacroModel format
- .mmod - MacroModel format
- .mol2 - Sybyl Mol2 format
- .mol - MDL MOL format
- .mopcrt - MOPAC Cartesian format
- .mopout - MOPAC Output format
- .mpd - Sybyl descriptor format
- .mpqc - MPQC output format
- .msm - MSI ChemNote format
- .nwo - NWChem output format
- .pc - PubChem format
- .pdb - Protein Data Bank format
- .pqs - Parallel Quantum Solutions format
- .prep - Amber Prep format
- .qcout - Q-Chem output format
- .res - ShelX format
- .rxn - MDL RXN format
- .sd - MDL MOL format
- .sdf - MDL SDF format
- .skc - ISIS Sketch
- SMARTS
- .smd - SMD 4.2
- .smi - SMILES format
- .tgf - ISIS Transp Graph
- .tmol - TurboMole Coordinate format
- .unixyz - UniChem XYZ format
- .vmol - ViewMol format
- .xml - General XML format
- .xyz - XYZ cartesian coordinates format
- .yob - YASARA.org YOB format