ICM Browser is a program for molecular modeling and high-performance molecular visualization and animation. A commercial version, ICM Browser Pro, has additional capabilities relating to creating, storing and sharing structural, biological and chemical information.

Indigo is a cheminformatics toolkit that includes a rendering library (Dingo), generation of canonical SMILES (Cano), an Oracle cartidge for searching molecular databses (Bingo) and R-Group deconvolution (Deco). It also can handle nucleotides (Nucleo).

Intocham converts from InsightII .car format to Charmm, Amber or Moil formats.

Isotopic Pattern Calculator is a small tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence. Furthermore, it can use Gnuplot to visualise the results.

Jaguar is an ab initio electronic structure software package that provides chemical accuracy for realistic systems, with particular strength in treating metal-containing systems. Calculations are efficient and scale well with molecular size.

Jana2000 is a system for solving and refinement of regular, modulated and composite structures from monocrystal and powder diffraction data.

JChem is a Java tool for developing applications that manipulate mixed chemical and corporate data. It supports most operating systems, database handlers, and web servers. JChem is an excellent tool for developing distributed custom chemical applications that can be accessed by web browsers.

JChemPaint is a Java program for drawing 2D chemical structures. It can load and save in CML format, export as bitmap and SVG, and automatically layout structures.

JMap3d takes volumetric data (particularly electron density data) and polygonises them, in order to produce up to five iso-surfaces. The result is written to a VRML97 (VRML2.0) file, which can then be viewed with any VRML viewer of your choice or with the included Java3D VRML viewer (from the Java3D & VRML working group).

JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures.