[BiO BB] Best Bioinformatics and Database Education

Thu Oct 30 15:30:09 EST 2003

Hi Group,

As a C++, VB, .NET programer, also experienced in SQL
I'm very interested to get into the bioinformatics
either in programming or in database architecture,
administration.

What are the modules I should get used to (I've heard
of Bioperl) ?

Is a certification in Biology or similar mandatory?

Thank you 

Denis

On Thu, 30 Oct 2003 12:01:33 -0500 (EST),
bio_bulletin_board-request at bioinformatics.org wrote:

> 
> When replying, PLEASE edit your Subject line so it is
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> Today's Topics:
> 
>    1. Molecular Mechanics (Universal Force Fields
> models) (Miguel Pignatelli)
> 
> --__--__--
> 
> Message: 1
> From: "Miguel Pignatelli" <Pignatelli at noraybio.com>
> To: <bio_bulletin_board at bioinformatics.org>
> Date: Thu, 30 Oct 2003 10:43:03 +0100
> Subject: [BiO BB] Molecular Mechanics (Universal Force
> Fields models)
> Reply-To: bio_bulletin_board at bioinformatics.org
> 
> This is a multi-part message in MIME format.
> 
> ------=_NextPart_000_0033_01C39ED2.984F9920
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> 	charset="iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
> 
> 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.
> =20
> The software imput will be atoms and coordinates, so
it
> will determine =
> which atoms are bonded. Is there any efficient
> algorithm for that?
> =20
> Any suggestions?
> 
> Thanks all
> 
> ------=_NextPart_000_0033_01C39ED2.984F9920
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> 
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0
> Transitional//EN">
> <HTML><HEAD>
> <META content=3D"text/html; charset=3Diso-8859-1" =
> http-equiv=3DContent-Type>
> <META content=3D"MSHTML 5.00.3809.1800"
> name=3DGENERATOR>
> <STYLE></STYLE>
> </HEAD>
> <BODY bgColor=3D#ffffff>
> <DIV><FONT face=3DArial size=3D2>
> <DIV><FONT face=3DArial size=3D2>Hi,</FONT></DIV>
> <DIV> </DIV>
> <DIV><FONT face=3DArial size=3D2>I'm trying to make a
> program in C=20
> that calculates the energy of a molecule from the
> coordinates X,Y,Z =
> of its=20
> atoms. We want to apply the Universal Force Fields
> (UFF) described by =
> Rappe.=20
> Once we have the total energy of the molecule
> (contribution from each =
> chemical=20
> bond (bond stretching), angle bending, torsional
terms,
> improper=20
> torsions, out of plane bending motions and
> non-bonded interactions=20
> (electrostatic and Van der Waals forces)) we will look
> for energy =
> minimisation=20
> through the conjugate gradient minimisation
> method.</FONT></DIV>
> <DIV> </DIV>
> <DIV><FONT face=3DArial size=3D2>I am looking for a
> similar software to =
> look at or=20
> any algorithm that could help me. First of all I would
> like to know what =
> is the=20
> best data structure to use in this kind of software
and
> if there is any =
> similar=20
> software to look at its code or any algorithm that
> implements the=20
> UFF.</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>The software imput
> will be atoms and =
> coordinates,=20
> so it will determine which atoms are bonded. Is there
> any efficient =
> algorithm=20
> for that?</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>Any
> suggestions?</FONT></DIV>
> <DIV> </DIV>
> <DIV><FONT face=3DArial><FONT size=3D2>Thanks=20
> all</FONT></FONT></DIV></FONT></DIV></BODY></HTML>
> 
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> 
> 
> 
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