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Lasko, Slovenia

University of Primorska is the third university in Slovenia. It is located in Koper, Izola, and Portorož and is named for the Slovenian Littoral region , where it is located. Wikipedia.

Konc J.,Slovenian National Institute of Chemistry | Janezic D.,Slovenian National Institute of Chemistry | Janezic D.,University of Primorska
Bioinformatics | Year: 2010

Motivation: Exploitation of locally similar 3D patterns of physico-chemical properties on the surface of a protein for detection of binding sites that may lack sequence and global structural conservation. Results: An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database of protein 3D structures and detects with sub-residue precision, structurally similar sites as patterns of physicochemical properties on the protein surface. Using an efficient maximum clique algorithm, the program identifies proteins that share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural similarity scores are calculated for the query protein's surface residues, and are expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein-protein, protein-small ligand and protein-DNA binding sites. Availability: The software is available, as a web tool, free of charge for academic users at http://probis.cmm.ki.si. Contact: dusa@cmm.ki.si. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press.

Konc J.,Slovenian National Institute of Chemistry | Janezic D.,University of Primorska
Nucleic Acids Research | Year: 2014

The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki. si/ligands. © 2014 The Author(s).

Simunic B.,University of Primorska
Journal of Electromyography and Kinesiology | Year: 2012

Tensiomyography is a method for valid and non-invasive estimation of skeletal muscle fibre type composition. The validity of selected temporal tensiomyographic measures has been well established recently; there is, however, no evidence regarding the method's between-day reliability. Therefore it is the aim of this paper to establish the between-day repeatability of tensiomyographic measures in three skeletal muscles. For three consecutive days, 10 healthy male volunteers (mean ± SD: age 24.6 ± 3.0. years; height 177.9 ± 3.9. cm; weight 72.4 ± 5.2. kg) were examined in a supine position. Four temporal measures (delay, contraction, sustain, and half-relaxation time) and maximal amplitude were extracted from the displacement-time tensiomyogram. A reliability analysis was performed with calculations of bias, random error, coefficient of variation (CV), standard error of measurement, and intra-class correlation coefficient (ICC) with a 95% confidence interval. An analysis of ICC demonstrated excellent agreement (ICC were over 0.94 in 14 out of 15 tested parameters). However, lower CV was observed in half-relaxation time, presumably because of the specifics of the parameter definition itself. These data indicate that for the three muscles tested, tensiomyographic measurements were reproducible across consecutive test days. Furthermore, we indicated the most possible origin of the lowest reliability detected in half-relaxation time. © 2012 Elsevier Ltd.

Stevanovic S.,University of Primorska | Stevanovic S.,University of Nis
Renewable and Sustainable Energy Reviews | Year: 2013

Passive solar design strategies comprise important ways of reducing the heating, cooling and lighting energy consumption of buildings. Although it is relatively simple to reduce the energy use up to some extent by applying individual strategies, very high levels of energy performance require application of the optimal combination of several strategies, verified through building energy simulations. Here we give an exhaustive review of the previous studies of simulation-based optimization of passive solar design strategies, with particular focus on recent research results. © 2013 Elsevier Ltd.

Konc J.,Slovenian National Institute of Chemistry | Konc J.,U.S. National Institutes of Health | Janezic D.,University of Primorska
Current Opinion in Structural Biology | Year: 2014

While structural genomics resulted in thousands of new protein crystal structures, we still do not know the functions of most of these proteins. One reason for this shortcoming is their unique sequences or folds, which leaves them assigned as proteins of 'unknown function'. Recent advances in and applications of cutting edge binding site comparison algorithms for binding site detection and function prediction have begun to shed light on this problem. Here, we review these algorithms and their use in function prediction and pharmaceutical discovery. Finding common binding sites in weakly related proteins may lead to the discovery of new protein functions and to novel ways of drug discovery. © 2013 Elsevier Ltd.

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