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Items: 1 to 20 of 60

1.

Tally-2.0: upgraded validator of tandem repeat detection in protein sequences.

Perovic V, Leclercq JY, Sumonja N, Richard FD, Veljkovic N, Kajava AV.

Bioinformatics. 2020 Feb 25. pii: btaa121. doi: 10.1093/bioinformatics/btaa121. [Epub ahead of print]

PMID:
32096820
2.

Deciphering Imidazoline Off-Targets by Fishing in the Class A of GPCR field.

Djikic T, Vucicevic J, Laurila J, Radi M, Veljkovic N, Xhaard H, Nikolic K.

Mol Inform. 2020 Feb 20. doi: 10.1002/minf.201900165. [Epub ahead of print]

PMID:
32078760
3.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

4.

Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR).

Sencanski M, Glisic S, Šnajder M, Veljkovic N, Poklar Ulrih N, Mavri J, Vrecl M.

Sci Rep. 2019 Nov 12;9(1):16555. doi: 10.1038/s41598-019-52934-8.

5.

DisProt: intrinsic protein disorder annotation in 2020.

Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D.

Nucleic Acids Res. 2020 Jan 8;48(D1):D269-D276. doi: 10.1093/nar/gkz975.

PMID:
31713636
6.

DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis.

Davidović R, Perovic V, Gemovic B, Veljkovic N.

Bioinformatics. 2019 Nov 8. pii: btz836. doi: 10.1093/bioinformatics/btz836. [Epub ahead of print]

PMID:
31702762
7.

Recent In Silico Resources for Drug Design and Discovery.

Veljkovic N.

Curr Med Chem. 2019;26(21):3836-3837. doi: 10.2174/092986732621190919104301.

PMID:
31584358
8.

Automated feature engineering improves prediction of protein-protein interactions.

Sumonja N, Gemovic B, Veljkovic N, Perovic V.

Amino Acids. 2019 Aug;51(8):1187-1200. doi: 10.1007/s00726-019-02756-9. Epub 2019 Jul 5.

PMID:
31278492
9.

Virtual Screen for Repurposing of Drugs for Candidate Influenza a M2 Ion-Channel Inhibitors.

Radosevic D, Sencanski M, Perovic V, Veljkovic N, Prljic J, Veljkovic V, Mantlo E, Bukreyeva N, Paessler S, Glisic S.

Front Cell Infect Microbiol. 2019 Mar 26;9:67. doi: 10.3389/fcimb.2019.00067. eCollection 2019.

10.

Functional characterization of β2-adrenergic and insulin receptor heteromers.

Susec M, Sencanski M, Glisic S, Veljkovic N, Pedersen C, Drinovec L, Stojan J, Nøhr J, Vrecl M.

Neuropharmacology. 2019 Jul 1;152:78-89. doi: 10.1016/j.neuropharm.2019.01.025. Epub 2019 Jan 29.

PMID:
30707913
11.

Genetic Markers for Coronary Artery Disease.

Veljkovic N, Zaric B, Djuric I, Obradovic M, Sudar-Milovanovic E, Radak D, Isenovic ER.

Medicina (Kaunas). 2018 May 28;54(3). pii: E36. doi: 10.3390/medicina54030036. Review.

12.

IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins.

Perovic V, Sumonja N, Marsh LA, Radovanovic S, Vukicevic M, Roberts SGE, Veljkovic N.

Sci Rep. 2018 Jul 12;8(1):10563. doi: 10.1038/s41598-018-28815-x.

13.

Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes.

Gemovic B, Sumonja N, Davidovic R, Perovic V, Veljkovic N.

Curr Med Chem. 2019;26(21):3890-3910. doi: 10.2174/0929867325666180214113704. Review.

PMID:
29446725
14.

Ibuprofen as a template molecule for drug design against Ebola virus.

Paessler S, Huang C, Sencanski M, Veljkovic N, Perovic V, Glisic S, Veljkovic V.

Front Biosci (Landmark Ed). 2018 Jan 1;23:947-953.

PMID:
28930583
15.

Corrigendum: DisProt 7.0: a major update of the database of disordered proteins.

Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. No abstract available.

16.

DisProt 7.0: a major update of the database of disordered proteins.

Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28. Erratum in: Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124.

17.

Predicted Enhanced Human Propensity of Current Avian-Like H1N1 Swine Influenza Virus from China.

Veljkovic V, Veljkovic N, Paessler S, Goeijenbier M, Perovic V, Glisic S, Muller CP.

PLoS One. 2016 Nov 9;11(11):e0165451. doi: 10.1371/journal.pone.0165451. eCollection 2016.

18.

TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation.

Perovic V, Sumonja N, Gemovic B, Toska E, Roberts SG, Veljkovic N.

Bioinformatics. 2017 Jan 15;33(2):289-291. doi: 10.1093/bioinformatics/btw590. Epub 2016 Sep 7.

19.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

20.

A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin.

Vucicevic J, Srdic-Rajic T, Pieroni M, Laurila JM, Perovic V, Tassini S, Azzali E, Costantino G, Glisic S, Agbaba D, Scheinin M, Nikolic K, Radi M, Veljkovic N.

Bioorg Med Chem. 2016 Jul 15;24(14):3174-83. doi: 10.1016/j.bmc.2016.05.043. Epub 2016 May 24.

PMID:
27265687

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