The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data.
ASAView is an algorithm, an application and a database of schematic representations of solvent accessibility of amino acid residues within proteins. A characteristic two-dimensional spiral plot of solvent accessibility provides a convenient graphical view of residues in terms of their exposed surface areas. In addition, sequential plots in the form of bar charts are also provided. Online plots of the proteins included in the entire Protein Data Bank (PDB), are provided for the entire protein as well as their chains separately.
ArgusLab is a molecular modeling, graphics, and drug design program.The ArgusDock docking engine, implemented in ArgusLab4.0, approximates an exhaustive search method, with similarities to DOCK and Glide. Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node (group of bonded atoms that do not have rotatable bonds) is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created. For each rotation, torsions in breadth-first order are constructed and those poses that survive the torsion search are scored. The N-lowest energy poses are retained and the final set of poses undergoes coarse minimization, re-clustering and ranking.
Thompson, M. A. (2004).
Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function.
ACS meeting, Philadelphia, 172, CINF 42, PA.
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.
The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates’ Alchemy and Sybyl Mol2 formats, Molecular Design Limited’s (MDL) Mol file format, Minnesota Supercomputer Center’s (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. It displays the molecule in various representations and allows one to rotate the molecule interactively.
Future releases of RasMol will continue to offer the GPL and RASLIC as alternative licenses for the source code, but, in order to conform to the license conditions of various libraries to which executables may be linked, starting with RasMol 2.7.5 release, the GPL is the only valid license to use the binary distributions.
Stat-200 is a remarkably comprehensive general statistics package. It incorporates all the descriptive statistics, parametric and non-parametric statistical tests, graphics and data transforms you will need for processing, analyzing and presenting data. Parametric tests and procedures in Stat-200 total 60 and there are 66 non-parametric tests and procedures and 30 different descriptive statistics. ANOVA is comprehensive and includes general N factor analysis. Many unusual procedures are included e.g. survival analysis. All tests have associated information windows which give literature references and other facts to assist in getting the right one for the job. Probabilities are calculated directly so there is no need to use tables
