Mansoor Saqi
Bioinformatics Group, Dept of Biomolecular Structure, Glaxo Group
Research, Greenford, Middlx. UK
Molecular Modelling of Eosinophil Derived Nuerotoxin (EDN)
The starting point is an alignment of EDN with 1onc (PANCREATIC
RIBONUCLEASE) and with 3rn3 (RIBONUCLEASE A). The sequence alignment
required manual adjustment in places but, apart from this, the approach
adopted was to generate amodel using minimal human intervention. Two
models were generated from the same alignment:
- (i) Model 1 was built using the Quanta (Molecular Simulations Inc.)
software for modelling the backbone. Loops were generated using the
Quanta fragment searching tool and assessed on the criteria of rms fit
to the stem and on bad contacts. The sidechains were modelled, outside
of Quanta, automatically, with the algorithm of Leach (J. Mol Biol
1994, 235, 345-56).
- (ii) Model 2 was generated from the same alignment, with the
automatic modelling program ProMod (Manual Peitsch, Glaxo Institute for
Molecular Biology, Geneva). ProMod can be accessed through SwissModel
on the ExPASy server
(URL:http://expasy.hcuge.ch/) and reuires no human intervention at all.
This allows comparison of loop modelling and sidechain packing
procedures with Model 1.
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