Quantum is a pure physics based molecular docking software which calculates Kd of a protein-ligand complex, and ligand position in the protein active site. This enables virtual screening of compound libraries. The calculation takes into account metals and other hetatoms in the protein active site as well as protein flexibility.

QuteMol is an open source (GPL), interactive, high quality molecular visualization system that aims to improve clarity and provide an easier understanding of the 3D shape and structure of large molecules or complex proteins. Its features include real time ambient occlusion, depth-aware silhouette enhancement, and automatic generation of animated gifs of rotating molecules for web page animations.

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

UCB-Enhanced Rasmol is based on Rasmol 2.6 with enhancements added. These enhancements include: multiple molecules can be viewed, part of a molecule can be rotated around a bond, distances/angles can be measured and the labels displayed.

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.

Rave is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging. It also contains tools for the detection of secondary structure elements in macromolecular electron-density maps.

RedMD (Reduced Molecular Dynamics) is an open source package for molecular dynamics simulations and normal mode analysis for coarse-grained models of proteins and nucleic acids. Force fields are based on one-bead elastic network models and their extensions. The code is written in C/C++ and is parallelized.

RM1 (Recife Model 1) is a reparameterisation of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. It is distributed as an external file for recent versions of MOPAC, as the default model for a modified version of the public domain MOPAC, and also can be implemented in HyperChem.

RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.

SCHAKAL is a FORTRAN program for the graphical representation of molecular and solid-state models.