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Dhir S.,Protein Structure and Bioinformatics | Pacurar M.,Protein Structure and Bioinformatics | Franklin D.,Federal University of Uberlandia | Gaspari Z.,Eotvos Lorand University | And 6 more authors.
Current Protein and Peptide Science | Year: 2010

SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al., Nucl. Acids. Res. 21:3111-3115, 1992). The current approach uses a curated collection of domain sequences - the SBASE domain library - and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics of the domain similarity network (http://hydra.icgeb.trieste.it/sbase/). It is especially useful in detecting rare, atypical examples of known domain types which are sometimes missed even by more sophisticated methodologies. This approach does not require multiple alignment or machine learning techniques, and can be a useful complement to other domain detection methodologies. This article gives an overview of the project history as well as of the concepts and principles developed within this the project. © 2010 Bentham Science Publishers Ltd. Source

Gaspari Z.,Eotvos Lorand University | Angyan A.F.,Eotvos Lorand University | Angyan A.F.,ELTE HAS Protein Modeling Group | Dhir S.,Protein Structure and Bioinformatics | And 4 more authors.
Current Protein and Peptide Science | Year: 2010

The emerging role of internal dynamics in protein fold and function requires new avenues of structure analysis. We analyzed the dynamically restrained conformational ensemble of ubiquitin generated from residual dipolar coupling data, in terms of protruding and buried atoms as well as interatomic distances, using four proximity-based algorithms, CX, DPX, PRIDE and PRIDE-NMR (http://hydra.icgeb.trieste.it/protein/). We found that Ubiquitin, this relatively rigid molecule has a highly diverse dynamic ensemble. The environment of protruding atoms is highly variable across conformers, on the other hand, only a part of buried atoms tends to fluctuate. The variability of the ensemble cautions against the use of single conformers when explaining functional phenomena. We also give a detailed evaluation of PRIDE-NMR on a wide dataset and discuss its usage in the light of the features of available NMR distance restraint sets in public databases. © 2010 Bentham Science Publishers Ltd. Source

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