Dear All
Due to I am working on a project I need some information.
Any of you are working on Grid computing And/Or Nanomedicine Or
Nanoinformatics?
Thanks!

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

Meeting Announcement
Automated Biorepositories: Successful Models

Dear colleagues,

LRIG will host a second annual meeting on biorepositories with an emphasis
on how automation has been successfully applied to solve problems with
managing collections. The meeting consists of a technology exhibition, tours
of RUCDR and social period followed by presentations and discussion. It will
take place at Rutgers, the State University of New Jersey in Piscataway, NJ
from 3:00-9:00 PM on February 28, 2008. The web page with full details may
be found at <http://lab-robotics.org/Mid_Atlantic/meetings/0802.htm>.

An abbreviated agenda:

Tours: Rutgers University Cell and DNA Repository (RUCDR)
Dr. David Toke, Associate Managing Director, Rutgers University Cell & DNA
Repository (RUCDR)

University Cell and DNA Repository.

Presentation: Development and validation of the UK Biobank sample handling,
processing and archiving protocol
Tim Peakman, Executive Director, UK Biobank

http://www.inforsense.com/index.php?id=204

Event: Unlock Insight from Your Clinical Data
Presenters Info: Hai Hu, Senior Director of Biomedical Informatics,
Windber Research Institute

Michael N. Liebman, Ph.D., Executive Director, Windber Research
Institute & President and Managing Director, Strategic Medicine, Inc

Mick Correll, Director Clinical Solutions, InforSense

Host: Dave Menninger, VP Marketing & Product Management, InforSense
Date: 19 September 2007
Time: 11:00 ET (New York)
Duration: 1 hour including Q&A

Description:

insurers, the healthcare industry continues to improve its
capabilities for electronic data capture. Despite these advances, a
gap remains in the ability of these IT systems to deliver knowledge
and insight back to the very researchers and clinicians they are built
to support.

Dear all,

We are happy to tell you that we just updated our Bioinformatics
journals section with cool new features !!!
1) A list of 20 Bioinformatics related journals. When it was possible
we associated to each journal, The web address, the impact factor, The
RSS/Feed address and a view at a glance of the articles of the current
issue.
2) The second sub-section contains a Google search engine that enables
you to perform a search restricted to these Bioinformatics journals.

The dedicated address is :
http://www.bioinformatics.fr/journals.php

And we made it printer friendly in case you want to read it during
your coffee break.

Hope you will enjoy it.
If your favorites bioinformatics journal is missing do not hesitate to
let us know.

Cheers,

The Bioinfomatics.fr team

Hi guys,

Just to let you know that we recently launched two Google maps
dedicated to Bioinformatics jobs and Bioinformatics events. So now it
will be very easy to check if there is an available position or an
upcoming event next to your place.
The two Google maps are available at the following address :

Bioinformatics job map :
http://www.bioinformatics.fr/jobs.php?mapview

Bioinformatics events map :
http://www.bioinformatics.fr/events.php?mapview

Kind Regards,

The Bioinformatics.fr team

I wish to introduce the OPTIMIZER web-server that optimizes the codon usage of a gene to increase its expression level. This web-server is focused on the heterologous, or even homologous, gene expression in bacterial hosts. Two indices, CAI and ENc (effective number of codons), are used to measure the optimization process.
Three methods of optimization are available:
- The 'one amino acid - one codon' method.
- A guided random method based on a Monte Carlo algorithm.
-The ‘customized one amino acid - one codon’ designed to maximize the optimization with the fewest changes in the query sequence.
One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using the following pre-computed tables from more than 150 prokaryotic species...

I wish to introduce the TOPD/FMTS software to evaluate similarities and differences between phylogenetic trees. TOPD/FMTS can compare trees with leaf-sets that either completely or partially overlap and can be also used to compare two trees, one or both of which are multigene family trees.

The version 1.0 of TOPD/FMTS implements the following methods to compare phylogenetic trees:
- Split distance.
- Nodal distance.
- Disagree.
- Taxa in common.
- Quartets.
- Triplets.

Each option is also complemented with a randomisation analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation.

TOPD/FMTS is freely available at: http://genomes.urv.cat/topd .
For more details see the article Puigbo et al. 2007. Bioinformatics doi: 10.1093/bioinformatics/btm135 .

--------------------------------------------------------------------------------------------------------------------
Pere Puigbò Avalos, PhD Student
Evolutionary Genomics Group,
Biochemistry and Biotechnology Department,
Rovira i Virgily University.
C/Marcel·lí domingo s/n. 43007. Campus Sescelades. Tarragona.