Laboratory of Structural Chemistry and Biology Laboratory of Structural Chemistry and Biology

Eötvös Loránd University, Institute of Chemistry, Budapest, Hungary
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Computational analysis of protein structural features & genomes

The PRIDE2 method & server
The PRIDE2 (PRobability of IDEntity 2) method is a fast protein-protein structure comparison algorithm based on the statistical comparison of Cα-Cα distance distributions in the structures examined. PRIDE2 is actually an improved version of the original PRIDE method including improved statistical background and handling of input structures. The PRIDE2 web server is available at: http://hydra.icgeb.trieste.it/pride


Cooperation: Dr. Sándor Pongor, Protein Structure and Bioinformatics group, ICGEB, Trieste

Publications
Zoltán Gáspári, Kristian Vlahovicek and Sándor Pongor:
Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.
Bioinformatics, 21(15):3322-3323.
[abstract]

CCA+, the CD Spectrum Analyser System

CCA+ (Convex Constraint Algorithm) is a program to analyze circular dichroism spectra of various chemical compounds, primarily proteins. It is maintained by our former laboratory member Imre Jákli. CCA+ has over 500 citations and 700 registered users worldwide. It is available at: http://www.chem.elte.hu/departments/protnmr/cca


Publications


Several aspects of genome evolution
This research area, connected only loosely to the main research focus of the lab, is done with intensive cooperations with members of several bioinformatics groups involving the study of various topics.

Main cooperation: Dr. Gábor Tóth Bioinformatics Group, Agricultural Biotechnology Center, Gödöllõ, Hungary

Publications
Csaba Ortutay, Zoltán Gáspári, Gábor Tóth, Edit Jáger, Gábor Vida, László Orosz and Tibor Vellai:
Speciation in Chlamydia: Genome-wide phylogenetic analyses identified a reliable set of acquired genes
J. Mol. Evol. 57(6): 672-680.
[abstract] [full text] [supplementary material]

Gábor Tóth, Zoltán Gáspári and Jerzy Jurka:
Microsatellites in different eukaryotic genomes: survey and analysis
Genome Res. (2000) 10(7):967-981.
[abstract] [full text] [supplementary material: SSRDB]
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