iNA is a computational tool for quantitative analysis of fluctuations in biochemical reaction networks. Such fluctuations, also known as intrinsic noise, arise due to the stochastic nature of chemical reactions and cannot be ignored for when some molecules are present only in very low copy numbers as is the case in living cells. The SBML-based software computes statistical measures such as means and standard deviations of concentrations within a given accuracy using the analytical system size expansion. The result of iNA’s analysis can be tested against the computationally much more expensive stochastic simulation algorithm.
SLD Calculator is a GUI to calculate the characteristics of chemical compounds, especially the Neutron and X-Ray scattering length densities that are often required to know in scattering experiments. Furthermore, it offers internationalization support and is capable of switching the language at runtime.
libcfp analyzes and parses the syntax of a user-supplied chemical formula in ASCII notation. It does not know anything about the semantics of real world physical element characteristics. But it requires no external library dependencies and uses namespace std:: only. Furthermore, it uses UnitTest++ during development to ensure consistent behavior of formula parsing.
Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results (populations and reaction counts) in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program. Solvers are implemented as command line executables, which makes it easy to launch batch jobs and simplifies the process of adding new solvers. Solvers include Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, Tau-leaping, and Hybrid direct/tau-leaping.
ChemDoodle is a fully functional chemical drawing application. In addition to being multi-platform, it natively reads and writes many common file formats, including ChemDraw's CDX and CDXML. It provides a number of widgets, a complete templating system, and access to public databases of common molecules.
LigandScout allows for sophisticated 3D pharmacophore generation from macromolecule-ligand complexes, pharmacophore overlay and interpolation, and a lightning fast and robust pharmacophore-based alignment algorithm that allows creating consensus pharmacophores and merged feature pharmacophores.