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Hello,
I am having trouuble with missing residues in pdb files and need to
replace them (i.e. interpolate them) using a program. I think swiss-
pdbviewer and pymol do that. My problem is that I am not very capable
of using those programs and the person whom I asked for help told me
that I have to check for missing residues in pdb file, open swiss-
pdbviewer then add residue at correct place and finally she told me
that I might need to do an energy minimization and I am thinking that
I will definitely do a mistake there. I was wondering if anyone knows
a more automated way to get the missing residues inserted for me
because I am thinking that you can find missing residues in pdb and
and programs can read that info and add these missing residues
themselves automatically.. (but again maybe not...

Hi all
I just have a simple question. What is the deffernce(s) between
lattice and off-lattice models in protein folding simulations.

Thank you

Hi Vladimir ,

The problem with docking inorganic molecules into protein structures is with
at atom typing ie Charges to be placed on the atoms..fully charged, partial
charges. Most forcefields are either biased to proteins or inorganic
molecules and metals. There is no comprehensive forcefield that covers all.
You will need to check the forcefield library for the atoms and molecules
covered. In general people approximate the charges. Run the expts, see if
the molecule is distorted. Rerun expts to overcome after charge
modifications for adjusting the distortions.

regards,

Sunil.

On 31/05/2008, molmodel-request@oat.bio.indiana.edu <
molmodel-request@oat.bio.indiana.edu> wrote:

Dear Sudha,

There are no real programs that "docks" inorganic molecules. The best way to
handle this is usually you place the molecule in the binding site, set up
the forcefields (ie Charges on the molecule), you can add restraints if you
know which residues/atoms it co-ordinates to and run MD simulation.

regards,

Sunil.

On 19/05/2008, molmodel-request@oat.bio.indiana.edu <
molmodel-request@oat.bio.indiana.edu> wrote:

I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
protein molecule. I could not locate any docking software which can
handle in organic molecule. If anyone can help me in this regard.
Thanks

Sudha

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Dear all,

We announce the release of NQ-Flipper, a public service for the
visualization and correction of unfavorable/incorrect asparagine
and glutamine side-chain rotamers. For further information on the
NQ-rotamer problem and the NQ-Flipper service see

Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable
interactions in protein folds.
Bioinformatics Advance Access published online on March 29, 2008.
http://dx.doi.org/10.1093/bioinformatics/btn108

Weichenberger & Sippl (2007) Recognition and Correction of Erroneous
Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
http://dx.doi.org/10.1093/nar/gkm263

NQ-Flipper is available as a public web service at
http://flipper.services.came.sbg.ac.at or may be downloaded as a
standalone application for Linux systems.

Enjoy!

Dear all,

We announce the release of NQ-Flipper, a public service for the
visualization and correction of unfavorable/incorrect asparagine
and glutamine side-chain rotamers. For further information on the
NQ-rotamer problem and the NQ-Flipper service see

Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable
interactions in protein folds.
Bioinformatics Advance Access published online on March 29, 2008.
http://dx.doi.org/10.1093/bioinformatics/btn108

Weichenberger & Sippl (2007) Recognition and Correction of Erroneous
Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
http://dx.doi.org/10.1093/nar/gkm263

NQ-Flipper is available as a public web service at
http://flipper.services.came.sbg.ac.at or may be downloaded as a
standalone application for Linux systems.

Enjoy!

We are pleased to announce the release of TopMatch-web, a public web
service for the alignment and superposition of protein structures and the
instant visualization of structural similiarities.

We believe that TopMatch is an exceptionally effective, accurate, and
enjoyable program for the investigation of protein structure similarities.

For further information and instructive examples see
Sippl & Wiederstein (2008)
A Note on Difficult Structure Alignment Problems.
Bioinformatics 24, pp. 426-427

TopMatch-web is available as a public web service at
http://topmatch.services.came.sbg.ac.at.

Enjoy!

The TopMatch Team
Center of Applied Molecular Engineering
University of Salzburg
Austria