Chemtool is a program for drawing organic molecules easily and store them as an X-Bitmap, Postscript and XFig file. It runs under X- Window and is written with GTK+.

Chimera is an extensible molecular modeling system that can be used for molecular visualisation, addition of hydrogens, volumetric data, displaying the results of MD simulations, viewing the output of DOCK, and it has support for writing extensions in the Python scripting language.

CHIMP (CHIMP Hierarchical Modeling Program) is a generic tool for the modeling of chemical phenomena. CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.

Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. It can also function as a helper application for web browsers and allows the web browser to show 3-dimensional structures from <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure>NCBI's Entrez</a> retrieval service.

CNS (Crystallography & NMR System) is a software suite designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.

COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules.

The Computational Crystallography Toolbox (cctbx) is a collection of fundamental procedures for Computational Crystallography. It includes a unit cell toolbox , a space group toolbox and an element toolbox for the handling of scattering factors and other element properties.

ConQuest is the primary program for searching and retrieving information from the Cambridge Structural Database (CSD). ConQuest provides a full range of text/numeric database search options, in addition to more complex search functionality including chemical substructure searching, geometrical searching, and intermolecular and non-bonded contact searching.

CONSCRIPT generates Gouraud shaded isosurfaces of protein electron density for high quality presentation in journals.

CORINA (COoRdINAtes), is a rule and data based system, that automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear code. CORINA offers many features to influence the 3D generation process, e.g. addition of lacking or implicitly given hydrogen atoms, neutralization of formal charges, orientation of the 3D structures according to their moments of inertia, removement of counter ions in salts.