ShaEP performs rigid-body superimposition of 3D molecular models. The user can specify several query structures on which to superimpose. Each input structure is overlaid on each query structure in turn and the superimposition corresponding to the highest similarity index is reported. ShaEP considers successive input structures with the same name (allowing a numbering suffix '_' or '-' followed by a number, i.e. 'mol', 'mol-1', and 'mol_2' are all understood as incarnations of 'mol') as conformations of the same molecule, and reports the highest similarity index over the set of conformers.

The output file is a regular ASCII text file that can be imported into a spreadsheet program. In addition, in the end of a run a hitlist file is produced that contains the names of maxhits compounds in the order of increasing similarity index (i.e., the best are the last). Optionally, a minimum similarity index limit (minHitSimilarity) can be set for a molecule to be included in the hitlist. The superimposed structures are output into a SDF file if structures option is given. The default is to omit the structures.

The superimposition is achived by first finding similarities in the molecular electrostatic potential (MEP) field, which results in a few candidate overlays. Starting from these initial superimpositions, the volume overlap of the structures and the MEPs are maximized. The overlap is calculated using a set of spherical Gaussian functions. The optimization algorithm is adapted from the TNPACK code of Schlick and co-workers (Schlick T and Fogelson A (1992) ACM Trans. Math. Softw. 18, 46-70 & 71-111; Xie D and Schlick T (1999) SIAM J. Opt. 10, 132-154; Xie D and Schlick T (1999) ACM Trans. Math. Softw. 25, 108-122.)

Usage examples

ShaEP lists available options when called with '-h' or '--help'.

Frequently asked questions