THREEDOM

THREEDOM is one of several programs provided in the INTERCHEM package which makes use of the Icosahedral Matching Algorithm (Peter Bladon. J. Mol. Graphics, 1989, 7, 130) for the comparison and alignment of structures. This application uses the algorithm as the final stage in 3D-database searching (c.f. V. J. van Geerestein, N.C. Perry, P. D. J. Grootenhuis, and C. A. G. Haasnoot. Tetrahedron Computer Methodology, 1990, 3, 595 [published1992]; N. C. Perry and V. J. van Geerestein. J. Chem. Inf. Comput. Sci., 1992, 32, 607).

Depending upon the circumstances the searching process can be preceeded by the use of a prefiltering stage; structures in the database having been previously characterised by prefilter parameters (molecular volume, size of longest molecular axis, eccentricity as measured by the ratios of the lengths of the principal molecular axes, logP values).

The full suite of programs for database searching comprises:-

• PREFILTERS. A program to calculate the filter parameters for structures in a database. This program is provided as a template, since experience has shown that changes in the FORTRAN code need to be made to cater for differences in data structures between databases.
  
• QUICKSCAN. The program which calculates the corresponding parameters for the target structure and then searches the database for "hits". This program has been updated recently to allow the option of generating alternative conformations of the "hit" structures.
  
• THREEDOM .This program is then applied to the "hits" (and any alternative corformations) extracted by QUICKSCAN to maximally align them with the target structure, and rank them in order of increasing similarity

Two other programs use the icosahedral matching algorithm:-

• COMPARISONS .This program allows a target structure to be compared with all the structures in a series of (up to ten) separate subdirectories.
  
• CORRELATE. A program which allows all the structures in one directory to be compared with all structures in a second (or the same) directory.

These are useful in situations (for example) where it is necessary to compare and group together multiple conformers of a single structure.

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Revised 18th July 2007