1. Docking of fatty acid substrates on an alphafold-predicted thioesterase from aureobasidium pullulans : final project paperEvgenija Gagaleska, 2026, diplomsko delo Ključne besede: molecular docking, binding site, enzymesubstrate interactions, protein–ligand binding, databases, structural bioinformatics, protein structure prediction, final project papers
Objavljeno v RUP: 07.08.2026; Ogledov: 327; Prenosov: 16
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2. Graphlet-based edge weighting for improved community detection in complex networksDziuba Anastasiia, Jure Pražnikar, 2026, izvirni znanstveni članek Opis: Community detection reveals the functional organization of complex networks. Unlike edge-based methods, graphlet-based approaches use higher-order structures, but most studies focus on common motifs or lack validation on networks with known communities. We evaluate eight small motifs on synthetic and real-world networks and propose a framework that weights node pairs by their graphlet co-occurrence while preserving original edges. This captures both direct connections and local topology, improving community detection. Our results show that graphlet-based weighting consistently enhances performance, but no single motif is best for all networks. Simpler motifs can perform as well as dense cliques, suggesting that relying only on cliques may miss important connectivity patterns.
Ključne besede: community, network, graphlets, small-motif
Objavljeno v RUP: 01.07.2026; Ogledov: 385; Prenosov: 10
Celotno besedilo (6,14 MB)
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3. Fast prediction of protein flexibilityJure Pražnikar, 2026, izvirni znanstveni članek Opis: Motivation Advances in hardware have made molecular dynamics (MD) simulations of protein structures faster and more accessible to the scientific community. However, accurately estimating protein flexibility using MD remains computationally demanding, especially for large systems and long time scales. Several MD-based resources—including MdMD, the DynamD database, and more recently ATLAS and mdCATH—now provide MD trajectories for thousands of proteins, enabling the development of predictive models. Results Here, the Graphlet Degree Vector (GDV) is introduced as a lightweight, fast, and easy-to-implement linear model for predicting protein flexibility directly from atom coordinates. GDV is a 15-dimensional feature vector that captures local packing and the spatial connectivity of each atom with its nearby neighbors. Trained on a subset of globular-like proteins from the ATLAS database, the GDV model achieves a Spearman correlation of 0.828 compared to MD data. The model trained on ATLAS dataset was further evaluated on independent Nuclear Magnetic Resonance and cryo-electron microscopy datasets, demonstrating the robustness and generalizability of the GDV-based approach. A key advantage of the GDV model is that it requires no additional external or experimental data and can be applied in near real time (on the order of 10 seconds) even for large proteins with 20,000 atoms on a standard desktop or laptop. Overall, the results show that a lightweight, fast, and purely coordinate-based model can provide accurate and generalizable predictions of protein flexibility across diverse folds and sizes.
Ključne besede: protein flexibility, graphlets, predictive model
Objavljeno v RUP: 16.04.2026; Ogledov: 605; Prenosov: 13
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7. Effects of time-restricted eating (early and late) combined with energy restriction vs. energy restriction alone on the gut microbiome in adults with obesityBernarda Habe, Tanja Črešnovar, Matjaž Hladnik, Jure Pražnikar, Saša Kenig, Dunja Bandelj, Nina Mohorko, Ana Petelin, Zala Jenko Pražnikar, 2025, izvirni znanstveni članek Opis: Background: Early time-restricted eating combined with energy restriction (eTRE + ER) has been shown to reduce fat mass, diastolic blood pressure (DBP) and fasting glucose more effectively than late TRE with energy restriction (lTRE + ER) or energy restriction (ER) alone. Given the gut microbiome’s sensitivity to circadian rhythms, we examined whether adding TRE, particularly eTRE, to ER alters gut microbiota composition beyond ER alone, and whether such effects persist during follow-up. Methods: We analysed anthropometric, biochemical and gut microbiome data from 76 participants at baseline and after a 3-month intervention (eTRE + ER: n = 33; lTRE + ER: n = 23; ER: n = 20). Follow-up microbiome data 6-months after the end of intervention were available for 43 participants. Gut microbiota composition was assessed via 16S rRNA gene sequencing of stool samples. Results: No significant between-group differences in beta diversity were observed over time. However, changes in alpha diversity differed significantly across groups at the end of the intervention (Shannon: F = 5.72, p < 0.001; Simpson: F = 6.72, p < 0.001; Richness: F = 3.99, p = 0.01) and at follow-up (Richness: F = 3.77, p = 0.02). lTRE + ER led to the greatest reductions in diversity post intervention, while ER was least favourable during follow-up. Although no significant between-group differences were observed at the phylum level either at the end of the intervention or during follow-up, only the eTRE + ER group exhibited a significant decrease in Bacillota and an increase in Bacteroidota during follow-up. At the genus level, differential abundance analysis revealed significant shifts in taxa such as Faecalibacterium, Subdoligranulum, and other genera within the Ruminococcaceae and Oscillospiraceae families. In the eTRE + ER, Faecalibacterium and Subdoligranulum increased, while in other groups decreased. Notably, the changes in Faecalibacterium were negatively correlated with fasting glucose, while the increase in Subdoligranulum was inversely associated with DBP; however, both associations were weak in strength. Conclusions: eTRE + ER may promote beneficial, lasting shifts in the gut microbiome associated with improved metabolic outcomes. These results support further research into personalized TRE strategies for treatment of obesity.
Ključne besede: eating window, energy restriction, microbiota, alpha and beta diversity, metabolic health, obesity
Objavljeno v RUP: 17.07.2025; Ogledov: 1504; Prenosov: 23
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