[BiO BB] Molecular Mechanics (Universal Force Fields models)

[val]

Hi Pete,
    Thanks for your comment.  Well generally, you are right. 
My point is a comparative inefficiency of the screening.
An experienced chemist can do much better, and the
reason is that energy is *not* a good/sensitive 
indicator of fine structural and functional effects
involved in discovery of the *successful* drug.
    This is why a successful drug takes huge efforts
to find - roughly $1B and 8-12 years, to me, an
indication of wrong approach.
    cheers,
val
    

----- Original Message ----- 
From: "Peter Oledzki" <biopolak at yahoo.co.uk>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Monday, November 03, 2003 8:57 AM
Subject: Re: [BiO BB] Molecular Mechanics (Universal Force Fields models)


> 
> Hello,
> 
> quoting you val "it does not help much in answering
> real questions in (bio)chemistry and bioinformatics"
> I would have to disagree these sort of calculations
> are used in structure based drug design all the time.
> The big pharma companies are using these sort of
> calculations to screen for lead componds and the
> preliminary results for current methods are
> encouraging.
> 
> Pete 
> 
> 
> 
>  --- val <val at vtek.com> wrote: > Hi Miguel,
> >     Google is your best friend.  Try, e.g., google
> > with
> > 'molecule energy software'.
> >     But i wouldn't rely much on this type of
> > calculation; it does not help much in answering real
> > questions in (bio)chemistry and bioinformatics.
> > my best,
> > val
> > 
> > 
> > ----- Original Message -----
> > From: Miguel Pignatelli
> > To: bio_bulletin_board at bioinformatics.org
> > Sent: Thursday, October 30, 2003 4:43 AM
> > Subject: [BiO BB] Molecular Mechanics (Universal
> > Force Fields models)
> > 
> > 
> > Hi,
> > 
> > I'm trying to make a program in C that calculates
> > the energy of a molecule
> > from the coordinates X,Y,Z of its atoms. We want to
> > apply the Universal
> > Force Fields (UFF) described by Rappe. Once we have
> > the total energy of the
> > molecule (contribution from each chemical bond (bond
> > stretching), angle
> > bending, torsional terms, improper torsions, out of
> > plane bending motions
> > and non-bonded interactions (electrostatic and Van
> > der Waals forces)) we
> > will look for energy minimisation through the
> > conjugate gradient
> > minimisation method.
> > 
> > I am looking for a similar software to look at or
> > any algorithm that could
> > help me. First of all I would like to know what is
> > the best data structure
> > to use in this kind of software and if there is any
> > similar software to look
> > at its code or any algorithm that implements the
> > UFF.
> > 
> > The software imput will be atoms and coordinates, so
> > it will determine which
> > atoms are bonded. Is there any efficient algorithm
> > for that?
> > 
> > Any suggestions?
> > 
> > Thanks all
> > 
> > _______________________________________________
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> 
> =====
> Peter Oledzki
> Department of Biochemistry and Molecular Biology
> University of Leeds,UK
> 
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