Subject: molecular shape and surfaces

From: [email-masked] (Robert Bywater)
Date: Tue, 11 Apr 95 15:04:20 +0200

Seongbin Park asks :

>I am looking for references about measure for surface complementarity
>between two molecules, especially protein/protein (or protein/ligand)
>Could anyone kindly give me such information ?

Since others may also be interested in this, I am sending my reply to
him over the net. There are many methods for studying surface
shape and complementarity, but the one I favour is the method of
shape descriptors based on spherical harmonics. Here are some
key references to publications in this field.  

Leicester S.E., Finney J.L., and Bywater R.P., Description of
molecular surface shape using Fourier descriptors. J. Mol. Graph. (~1988~) 
{\bf 6} 104-108. 

Leicester S.E., Finney J.L. and Bywater R.P., A quantitative
representation of molecular surface shape  i) Theory and development of the
method. {\em J. Math. Chem.} (~1994~) {\bf 16} 315-341.

Leicester S.E., Finney J.L. and Bywater R.P., A quantitative
representation of molecular surface shape ii) Protein classification using
Fourier descriptors and classical scaling. {\em J. Math. Chem.} (~1994~) 
{\bf 16} 343-365.

Max N.L. \& Getzoff E.D., Spherical harmonic molecular surfaces.
IEEE Comput. Graphics Appl. (~1998~) {\bf 8} 42-50.

Duncan B.S. \& Olson A.J., Approximation and Characterization of Molecular
Surfaces {\em Biopolymers} (~1993~) {\bf 33} 219-229.

The `shape' method gives a purely geometric description of molecular
surface shape, but there is more in store - watch out for new developments
that will alow the inclusion of charge and `hydrophobicity' in the
determination of surface complentarity being developed by myself and
colleagues. More info on this in about 1/2 a year from now.

regards

Robert Bywater

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