

......
Anyway, I have this program for doing similarity measurements/alignments,
that was based on the original SEAL (Steric and Electrostatic ALignment)
code of Kearsley and Smith.  My program (called 'walrus') uses a much
more sophisticated model for assessing the similarity, but this may be
regarded as overkill for most cases (each calculation on a small molecule
takes a few hours on an Octane; SEAL takes a few seconds) and is probably
best restricted to calibration.  It is also a pig to use.  And it takes
its input from Gaussian.  But please let me know if you are interested.

The SEAL code itself (fortran, but you need to make a couple of changes to
get it to compile on an SGI) was supplied on a floppy disk with the
original publication.  I had all sorts of trouble getting this (floppy
disks degrade quite quickly...), so, again, please let me know if you are
interested.

Good references to get you started are:

@article{kears:seal,
  author  = "S. K. Kearsley and G. M. Smith",
  title   = "An alternative method for the alignment of molecular
             structures: maximising electrostatic and steric overlap",
  journal = "Tetrahedron Computer Methodology",
  volume  = 3,
  pages   = "615--633",
  year    = 1990,
  note    = "Includes original Fortran-77 source code for SEAL program."}

@article{meyer:molecsim,
  author  = "A. Y. Meyer and W. G. Richards",
  title   = "Similarity of molecular shape",
  journal = "Journal of Computer-Aided Molecular Design",
  volume  = 5,
  pages   = "427--439",
  year    = 1991}

@article{richards:hrindex,
  author  = "E. E. Hodgkin and W. G. Richards",
  title   = "A semi-empirical method for calculating molecular similarity",
  journal = "Journal of the Chemical Society, Chemical Communications",
  pages   = "1342--1344",
  year    = 1986}

@incollection{dean:drugs,
  author  = "P. M. Dean",
  title   = "Defining molecular similarity and complementarity for drug design",
  booktitle="Molecular Similarity in Drug Design",
  pages   = "1--21",
  editor  = "P. M. Dean",
  publisher="Chapman and Hall",
  address = "London",
  year    = 1995}

@incollection{good:drugs,
  author  = "A. C. Good",
  title   = "3D molecular similarity indices and their application in
             {QSAR} studies",
  booktitle="Molecular Similarity in Drug Design",
  pages   = "1--21",
  editor  = "P. M. Dean",
  publisher="Chapman and Hall",
  address = "London",
  year    = 1995}

Being nearby, you might also like to look in my thesis, which should be in
the University of London library (C. S. Page, PhD, 1998).  The final
chapter ("Measuring Chirality") has a (fairly) comprehensive review.

Hope this helps.

best wishes,

Chris Page
Uni. Valencia