Section 3.3.3.2.9.  HYDRA

This program, due to Hubbard (1985) (and, more recently, to Molecular Simulations) has several functional parts, referred to as `heads', which all use the same data structure. The addition of further heads may be accomplished, knowing the data structure, without the need to know anything of the internal workings of existing heads.

The program contains extensive features for the display, analysis and modelling of molecular structure with particular emphasis on proteins. Display options include dotted surfaces, molecular skeletons, protein cartoons and a variety of van der Waals, ball-and-stick, and other raster-graphics display techniques such as ray tracing and shaded molecular surfaces. Protein analysis features include the analysis of hydrogen bonding, and of secondary and domain structure, as well as computational assessment of deviations from accepted protein structural characteristics such as abnormal main-chain or side-chain conformations and solvent exposure of hydrophobic amino acids. A full set of protein modelling facilities are provided including homology modelling and the `docking' of substrate molecules. The program contains extensive tools for interactive modelling of structures from NMR or X-ray crystallographic data, and provides interfaces to molecular-mechanics and dynamics calculations. There are also database searching facilities to analyse and compare features of protein structure, and it is well suited to the making of cine films.