Integration of molecular network data reconstructs Gene Ontology.

Motivation: Recently, a shift was made from using Gene Ontology (GO) to evaluate molecular network data to using these data to construct and evaluate GO. Dutkowski et al. provide the first evidence that a large part of GO can be reconstructed solely from topologies of molecular networks. Motivated by this work, we develop a novel data integration framework that integrates multiple types of molecular network data to reconstruct and update GO. We ask how much of GO can be recovered by integrating various molecular interaction data. Results: We introduce a computational framework for integration of various biological networks using penalized non-negative matrix tri-factorization (PNMTF). It takes all network data in a matrix form and performs simultaneous clustering of genes and GO terms, inducing new relations between genes and GO terms (annotations) and between GO terms themselves. To improve the accuracy of our predicted relations, we extend the integration methodology to include additional topological information represented as the similarity in wiring around non-interacting genes. Surprisingly, by integrating topologies of bakers’ yeasts protein–protein interaction, genetic interaction (GI) and co-expression networks, our method reports as related 96% of GO terms that are directly related in GO. The inclusion of the wiring similarity of non-interacting genes contributes 6% to this large GO term association capture. Furthermore, we use our method to infer new relationships between GO terms solely from the topologies of these networks and validate 44% of our predictions in the literature. In addition, our integration method reproduces 48% of cellular component, 41% of molecular function and 41% of biological process GO terms, outperforming the previous method in the former two domains of GO. Finally, we predict new GO annotations of yeast genes and validate our predictions through GIs profiling. Availability and implementation: Supplementary Tables of new GO term associations and predicted gene annotations are available at http://bio-nets.doc.ic.ac.uk/GO-Reconstruction/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Supplementary data for the article: Blagojević, J. P.; Janjić, G. V.; Zarić, S. D. Very Strong Parallel Interactions between Two Saturated Acyclic Groups Closed with Intramolecular Hydrogen Bonds Forming Hydrogen-Bridged Rings. Crystals 2016, 6 (4). https://doi.org/10.3390/cryst6040034

Supplementary material for: [https://doi.org/10.3390/cryst6040034]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1928

Microstructural evolution during friction stir welding of AlSi1MgMn alloy

This paper provides the research of the infl uence of geometric and kinematic parameters on the microstructure and mechanical properties of welded joint of aluminum alloy AlSi1MgMn (6082-T6) obtained through the Friction Stir Welding (FSW) process. The experiment parameters were welding speed, rotation speed, angle of pin slope, pin diameter and shoulder diameter. On the obtained welded workpieces the dynamic testing on the impact toughness, and determination of microstructural zones were carried out

Mikrostrukturni razvitak AlSi1MgMn slitine tijekom zavarivanja trenjem

This paper provides the research of the influence of geometric and kinematic parameters on the microstructure and mechanical properties of welded joint of aluminum alloy AlSi1MgMn (6082-T6) obtained through the Friction Stir Welding (FSW) process. The experiment parameters were welding speed, rotation speed, angle of pin slope, pin diameter and shoulder diameter. On the obtained welded workpieces the dynamic testing on the impact toughness, and determination of microstructural zones were carried out.U radu se istražuje uticaj geometrijskih i kinematskih parametara na mikrostrukturu i mehanička svojstva zavarenog spoja od aluminijske slitine AlSi-1MgMn (6082-T6) dobivene postupkom zavarivanja trenjem (ZT). Parametri provedenih pokusa su brzina zavarivanja, kutna brzina okretanja alata, kut nagiba trna, promjer trna i promjer čela alata. Kod dobivenih zavarenih uzoraka izvedena su dinamička ispitivanja na udarnu žilavosti i određene su mikrostrukturne zone

Supplementary data for the article: Janjić, G. V.; Milosavljević, M. D.; Veljković, D. Ž.; Zarić, S. D. Prediction of Strong O-H/M Hydrogen Bonding between Water and Square-Planar Ir and Rh Complexes. Physical Chemistry Chemical Physics 2017, 19 (13), 8657–8660. https://doi.org/10.1039/c6cp08796e

Supplementary material for: [https://doi.org/10.1039/c6cp08796e]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2444]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3230

Supplementary data for the article: Janjić, G. V.; Milosavljević, M. D.; Veljković, D. Ž.; Zarić, S. D. Prediction of Strong O-H/M Hydrogen Bonding between Water and Square-Planar Ir and Rh Complexes. Physical Chemistry Chemical Physics 2017, 19 (13), 8657–8660. https://doi.org/10.1039/c6cp08796e

Supplementary material for: [https://doi.org/10.1039/c6cp08796e]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2444]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3230

Supplementary data for the article: Antonijević, I. S.; Janjić, G. V.; Milčić, M. K.; Zarić, S. D. Preferred Geometries and Energies of Sulfur-Sulfur Interactions in Crystal Structures. Crystal Growth and Design 2016, 16 (2), 632–639. https://doi.org/10.1021/acs.cgd.5b01058

Supplementary material for: [https://doi.org/10.1021/acs.cgd.5b01058]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2042]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3596

Supplementary data for article: Malenov, D. P.; Janjić, G. V.; Veljković, D. Ž.; Zarić, S. Mutual Influence of Parallel, CH/O, OH/Pi and Lone Pair/Pi Interactions in Water/Benzene/Water System. Computational and Theoretical Chemistry 2013, 1018, 59–65. https://doi.org/10.1016/j.comptc.2013.05.030

Supplementary material for: [https://doi.org/10.1016/j.comptc.2013.05.030]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1390

Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-H..Se and C-H..S interactions (∼80%), notably less numerous are structures with Se..Se and S..S interactions (∼5%), and Se..π and S..π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-H..Se (∼-0.8 kcal mol-1) and C-H..S interactions are weaker than the most stable parallel interaction (∼-3.3 kcal mol-1) and electrostatic interactions of σ/π type (∼-2.6 kcal mol-1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-H..Se (∼-4.4 kcal mol-1) and N-H..Se interactions (∼-2.2 kcal mol-1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand. © 2020 International Union of Crystallography

Supplementary data for article: Vojislavljević-Vasilev, D.; Janjić, G. V.; Ninković, D.; Kapor, A.; Zarić, S. The Influence of Water Molecule Coordination onto the Water-Aromatic Interaction. Strong Interactions of Water Coordinating to a Metal Ion. CrystEngComm 2013, 15 (11), 2099–2105. https://doi.org/10.1039/c2ce25621e

Supplementary material for: [https://doi.org/10.1039/c2ce25621e]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1602