Bioinformatics

University of Salzburg

Salzburg | Website

Core facility (CF)

Short Description

The server infrastructure comprises 15 high-performance computers with multi-core processors (up to 3 GHz):
8 x HP ProLiant
1 x supermicro 4 U 2x4-corel
1 x supermicro 1U 2x10-core
1 x supermicro 2 U 2x10 core
1 x supermicro 1U 2x24-core
2 x HE Intel Dual CPU
1 x LYNX CALLEO

Use: Storage of protein structure data, calculation of protein classifications, derivation of energy functions for protein structure analysis, identification of transcription factor binding sites, immunoinformatics, etc.
In many cases, the results obtained are also made available to the scientific community as a web service.

The PC infrastructure comprises approx. 20 desktop computers (Linux, Windows, MacOS X)
Use: software development, data analysis, etc.

Contact Person

Assoc. Prof. Dr. Markus Wiederstein

Research Services

The methods developed at the CF (protein structure analysis, protein structure comparison, efficient protein structure search, immunoinformatics, etc.) are made available to the scientific community in the form of software and web services.

Methods & Expertise for Research Infrastructure

Storage of protein structure data
Calculation of protein classifications
Development of energy functions for protein structure analysis
Identification of transcription factor binding sites
Immunoinformatics
Software development
Data analysis

In many cases, the results obtained are also provided as a web service to the scientific community.

Assoc. Prof. Dr. Markus Wiederstein
Fachbereich Biowissenschaften
0043 662 8044 5794
markus.wiederstein@sbg.ac.at
https://plus.ac.at/lackner
Please contact us via science.plus@sbg.ac.at, or contact the responsible person for this section, mentioned in the contact field
Strukturbasierte Vorhersage von MHC II Bindepetiden
2017-2021
Peter Lackner, Josef Laimer
https://pbwww.services.came.sbg.ac.at/?page_id=762
MHCII3D-Robust Structure Based Prediction of MHC II Binding Peptides.
Laimer J, Lackner P. Int J Mol Sci. 2020 Dec 22;22(1):12. doi:
10.3390/ijms22010012.

Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in
IgE cross-reactivity of allergenic lipid transfer proteins.
Di Muzio M, Wildner S, Huber S, Hauser M, Vejvar E, Auzinger W, Regl C, Laimer
J, Zennaro D, Wopfer N, Huber CG, van Ree R, Mari A, Lackner P, Ferreira F,
Schubert M, Gadermaier G.
J Biol Chem. 2020 Dec 18;295(51):17398-17410. doi: 10.1074/jbc.RA120.014243.

Friend or Foe: Lipid Droplets as Organelles for Protein and Lipid Storage in Cellular Stress Response, Aging and Disease
Geltinger F, Schartel L, Wiederstein M, Tevini J, Aigner E, Felder TK, Rinnerthaler M
Molecules. 2020 Oct 30;25(21):5053. doi: 10.3390/molecules25215053.

In silico Design of Phl p 6 Variants With Altered Fold-Stability Significantly
Impacts Antigen Processing, Immunogenicity and Immune Polarization.
Winter P, Stubenvoll S, Scheiblhofer S, Joubert IA, Strasser L, Briganser C,
Soh WT, Hofer F, Kamenik AS, Dietrich V, Michelini S, Laimer J, Lackner P,
Horejs-Hoeck J, Tollinger M, Liedl KR, Brandstetter J, Huber CG, Weiss R.
Front Immunol. 2020 Aug 18;11:1824. doi: 10.3389/fimmu.2020.01824. eCollection
2020.

A hybrid of two major Blomia tropicalis allergens as an allergy vaccine
candidate.
da Silva ES, Aglas L, Pinheiro CS, de Andrade Belitardo EMM, Silveira EF,
Huber S, Torres RT, Wallner M, Briza P, Lackner P, Laimer J, Pacheco LGC, Cruz
ÁA, Alcântara-Neves NM, Ferreira F.
Clin Exp Allergy. 2020 Jul;50(7):835-847. doi: 10.1111/cea.13611

The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved
Cysteines) Domain-Proteins Are Conserved in the Green Lineage.
Nguyen-Kim H, San Clemente H, Laimer J, Lackner P, Gadermaier G, Dunand C,
Jamet E.
Int J Mol Sci. 2020 Apr 3;21(7):2488. doi: 10.3390/ijms21072488.

Retinoic acid-loading of the major birch pollen allergen Bet v 1 may improve specific allergen immunotherapy: In silico, in vitro and in vivo data in BALB/c mice.
Hufnagl K, Moussa Afify S, Braun N, Wagner S, Wallner M, Hauser M, Wiederstein M, Gadermaier G, Wildner S, Redegeld FA, Blokhuis BR, Hofstetter G, Pali-Schöll I, Roth-Walter F, Pacios LF, Jensen-Jarolim E.
Allergy. 2020 Aug;75(8):2073-2077. doi: 10.1111/all.14259.

TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D
2020
Wiederstein, M., Sippl M.J.
Nucleic Acids Research
https://academic.oup.com/nar/article-abstract/48/W1/W31/5849903

MAESTROweb: a web server for structure based protein stability prediction
2016
Laimer J., Hiebl-Flach J., Lengauer D., Lackner P.
Bioinformatics
http://bioinformatics.oxfordjournals.org/content/early/2016/01/27/bioinformatics.btv769.abstract

Structure-Based Characterization of Multiprotein Complexes
2014
Wiederstein M., Gruber M., Frank K., Melo F., Sippl M.J.
Structure
http://dx.doi.org/10.1016/j.str.2014.05.005

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
2013
Laimer J., Zuzan C.J., Ehrenberger T., Freudenberger M., Gschwandtner S., Lebherz C., Lackner P.
BMC Bioinformatics
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-140

Detection of spatial correlations in protein structures and molecular complexes
2012
Sippl M.J., Wiederstein M.
Structure
http://dx.doi.org/10.1016/j.str.2012.01.024

Real space refinement of crystal structures with canonical distributions of electrons
2011
Ginzinger S., Gruber M., Brandstetter H., Sippl M.J.
Structure
http://dx.doi.org/10.1016/j.str.2011.10.011

High-performance signal peptide prediction based on sequence alignment techniques
2008
Frank K., Sippl M.J.
Bioinformatics
http://dx.doi.org/10.1093/bioinformatics/btn422

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
2007
Wiederstein M., Sippl M.J.
Nucleic Acids Research
http://dx.doi.org/10.1093/nar/gkm290

NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
2007
Weichenberger C.X., Sippl M.J.
Nucleic Acids Research
http://dx.doi.org/10.1093/nar/gkm263