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Molecular modelling capabilities

George A. Heavner gheavner at voicenet.com
Sat Feb 22 17:42:24 EST 1997

Dr. Duncan Clark wrote:
> Can anyone give me an idea of what the current ability of molecular
> modelling programs is for small molecules. Can they give a reliable (ie
> pretty close to real life) model of say a peptide of 12 residues (ie
> phage display peptides) or what about a ss 80mer oligonucleotide?
> Many thanks
> Duncan
> --------------------------------------------------------------------------------
> The problem with being on the cutting edge is that you occasionally get
> sliced from time to time....
> Duncan Clark
> DNAmp Ltd.
> TEl/FAX 01252376288
> http://www.dnamp.com
> http://www.genesys.demon.co.uk

It may sound like a flippant answer but, in the absence of structural
constraints (e.g. disulfide bonds or other cyclic structures) or
experimental data that suggests or supports structural limitations (e.g.
distance or angle measurements) the modeling of a small peptide can be
whatever you would like it to be.  Many small peptides that have been
studied show a high degree of conformational mobility.  Even crystal
structures are not always unique for a single peptide.  One paper even
showed four different enkephalin conformations in the same crystal. 
Given the dynamics of the real world, in silico studies could do no
better.  As structures become larger, homology modeling begins to
approach "real life."

George A. Heavner
Senior Director, Peptide R&D
Centocor, Inc.

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