SCORE is an empirical method for estimating the binding affinity of a protein-ligand complex with known 3D structure. SCORE uses a linear equation to describe the binding energy changes upon the binding process, which includes terms accounting for hydrogen-bonding, hydrophobic effect, and deformation effect.

SHELX is a set of programs for crystal structure determination from single-crystal diffraction data.

SHELX-to-ORTEP converts SHELX output files to ORTEP format.

Siam Quantum is an ab initio quantum chemistry program that uses quantum mechanics to determine the total energy and wave function of molecules within the framework of the Hartee-Fock method. The source code and documentation was originally designed to introduce students to electronic structure calculations. It can perform geometry optimisation and simple population analysis. Further developments are ongoing.

SIMPSON is a General Simulation Program for Solid-State NMR. It features multi-pulse 1D/2D experiments on large spin-systems with input-files implemented using a simple scripting language. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, rf irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition.

simref is a structure refinement program for the simultaneous evaluation of several powder diffraction data sets and multiple phases per data set. With a structural model all calculated diffraction profiles are fitted to the corresponding observed diffraction profile by the method of least squares. This procedure is called Rietveld method (Rietveld, 1969 ). By the simultaneous refinement of several data sets new evaluation techniques are possible.

SimSoup is is a graphical artificial chemistry simulator. The program enables a chemistry to be defined in terms of molecule types and the possible interactions between them. A simulation run involves setting up a number of molecules of various molecule types in a reactor, and then allowing interactions to take place over a period of time.

Simulaid is a set of utilities to prepare molecular dynamics simulations. It features optimal solute placement, conversions between file formats and analysis of results.

The SIRware suite includes SIR97 (Direct Method program for the resolution and refinement of crystal structures using single crystal data), SIR2002 (Direct Method program for the resolution of proteins using single crystal data; can be used also for resolution and refinement of small and medium size crystal structures) and SIR2004 (automatic solution of crystal structures by Direct and Patterson Methods; it can be used both for resolution and refinement of small/medium size crystal structures and for macromolecules with data up to 1.4-1.5 Ang.)

Situs is an award-winning program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. The software supports both rigid-body and flexible docking using a variety of fitting strategies.