Apologies for the free editing:
> > <snip>
> > Molecular models are the result of numbers emerging from computer programs.
> > The results of such computations do not reflect anything in nature. There's
> > no experimental evidence whatsoever, making modelling a very theoretical --
> > in my eyes uninteresting -- exercise.
> > </snip>
>
> <snip>
> Because computational models don't have direct experimental data behind
> them, they need an even stronger external validation.
> </snip>
I do not understand this argument about the lack of experimental data
behind 'computational models': Even the so-called empirical force fields
are parametrised and optimised against solid experimental data and ab
initio quantum mechanical calculations (which makes me wonder: are quantum
mechanical calculations also devoid of any physical meaning according to
the views presented above ?).
To make this crystal clear: I do not understand why, for example, a pure
physics-based folding simulation of small protein which results in the
recording of a folding event should be treated with anything less than
pure enthusiasm, for it proves the level of detailed understanding of the
physical world encoded in these models.
Lastly, may I add that a significant portion of the PDB (the NMR
structures), are very heavily dependant on these same molecular mechanics
forcefields that are used for molecular modeling and simulation.
My twocents,
Nicholas
--
Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
