Application of Information Spectrum Method on Small Molecules and Target Recognition

Authors: Sencanski, Milan, Sumonja, Neven, Perovic, Vladimir, Glisic, Sanja, Veljkovic, Nevena, Veljkovic, Veljko

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1907.02713

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

Authors: Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, C., Dukka B K., Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio, del Pozo, Angela, Fernández, José M, Maietta, Paolo, Valencia, Alfonso, Tress, Michael L, Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W, van Dijk, Aalt DJ, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C, Vencio, Ricardo ZN, Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael JE, Wass, Mark N, Huntley, Rachael P, Martin, Maria J, O'Donovan, Claire, Robinson, Peter N, Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C, Brenner, Steven E, Linial, Michal, Orengo, Christine A, Rost, Burkhard, Greene, Casey S, Mooney, Sean D, Friedberg, Iddo, Radivojac, Predrag

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1601.00891

Functional characterization of β2-adrenergic and insulin receptor heteromers

Authors: Susec, Maja, Sencanski, Milan, Glisic, Sanja, Veljkovic, Nevena, Pedersen, Christina, Drinovec, Luka, Stojan, Jurij, Nøhr, Jane, Vrecl, Milka

Source: In Neuropharmacology 1 July 2019 152:78-89

Automated feature engineering improves prediction of protein–protein interactions

Authors: Sumonja, Neven, Gemovic, Branislava, Veljkovic, Nevena, Perovic, Vladimir

Source: Amino acids. 51(8):1187-1200

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100118377107.0x000001&indx=1&recIds=ETOCvdc_100118377107.0x000001

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

Authors: Gemovic, Branislava, Sumonja, Neven, Davidovic, Radoslav, Perovic, Vladimir, Veljkovic, Nevena

Source: Current medicinal chemistry. 26(21):3890-3910

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100090524847.0x000001&indx=1&recIds=ETOCvdc_100090524847.0x000001

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

Authors: Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy, Lee, Alexandra, Kacsoh, Balint, Crocker, Alex, Lewis, Kimberley, Georghiou, George, Nguyen, Huy, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca, Freddolino, Peter, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José, Gemovic, Branislava, Perovic, Vladimir, Davidović, Radoslav, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex, Antczak, Magdalena, Fabris, Fabio, Wass, Mark, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel, Reeb, Jonas, Ritchie, David, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio, Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage, Jo, Dane, Suh, Erica, Dayton, Jonathan, Larsen, Dallas, Omdahl, Ashton, McGuffin, Liam, Brackenridge, Danielle, Babbitt, Patricia, Yunes, Jeffrey, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti, Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven, Orengo, Christine, Jeffery, Constance, Bosco, Giovanni, Hogan, Deborah, Martin, Maria, O'Donovan, Claire, Mooney, Sean, Greene, Casey, Radivojac, Predrag, Friedberg, Iddo

Source: Genome biology. 20(1):1-23

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190701351.0x000001&indx=1&recIds=ETOCvdc_100190701351.0x000001

Genetic Markers for Coronary Artery Disease

Authors: Veljkovic, Nevena, Zaric, Bozidarka, Djuric, Ilona, Obradovic, Milan, Sudar-Milovanovic, Emina, Radak, Djordje, Isenovic, Esma R.

Source: Medicina. 54(3):390-402

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN617123909&indx=1&recIds=ETOCRN617123909

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

Authors: Perovic, Vladimir, Sumonja, Neven, Marsh, Lindsey, Radovanovic, Sandro, Vukicevic, Milan, Roberts, Stefan, Veljkovic, Nevena

Source: Scientific reports. 8(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100171371097.0x000001&indx=1&recIds=ETOCvdc_100171371097.0x000001

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

Authors: Vucicevic, Jelica, Srdic-Rajic, Tatjana, Pieroni, Marco, Laurila, Jonne M.M., Perovic, Vladimir, Tassini, Sabrina, Azzali, Elisa, Costantino, Gabriele, Glisic, Sanja, Agbaba, Danica, Scheinin, Mika, Nikolic, Katarina, Radi, Marco, Veljkovic, Nevena

Source: In Bioorganic & Medicinal Chemistry 15 July 2016 24(14):3174-3183

Influenza vaccine as prevention for cardiovascular diseases: Possible molecular mechanism

Authors: Veljkovic, Veljko, Glisic, Sanja, Veljkovic, Nevena, Bojic, Tijana, Dietrich, Ursula, Perovic, Vladimir R., Colombatti, Alfonso

Source: In Vaccine 12 November 2014 32(48):6569-6575

Deciphering Imidazoline Off‐targets by Fishing in the Class A of GPCR field

Authors: Djikic, Teodora, Vucicevic, Jelica, Laurila, Jonne, Radi, Marco, Veljkovic, Nevena, Xhaard, Henri, Nikolic, Katarina

Source: Molecular informatics. 39(7)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100107595072.0x000001&indx=1&recIds=ETOCvdc_100107595072.0x000001

Simple and General Criterion for 'in silico' Screening of Candidate HIV Drugs

Authors: Veljkovic, Nevena, Glisic, Sanja, Prljic, Jelena, Perovic, Vladimir, Veljkovic, Veljko

Source: Current pharmaceutical biotechnology. 14(5):561-569

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCETOCvdc_100027183782.0x000001&indx=1&recIds=ETOCETOCvdc_100027183782.0x000001

Natural Products as Promising Therapeutics for Treatment of Influenza Disease

Authors: Sencanski, Milan, Radosevic, Draginja, Perovic, Vladimir, Gemovic, Branislava, Stanojevic, Maja, Veljkovic, Nevena, Glisic, Sanja

Source: Current pharmaceutical design. 21(38):5573-5588

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100083497926.0x000001&indx=1&recIds=ETOCvdc_100083497926.0x000001

Improving attrition rates in Ebola virus drug discovery

Authors: Glisic, Sanja, Paessler, Slobodan, Veljkovic, Nevena, Perovic, Vladimir R, Prljic, Jelena, Veljkovic, Veljko

Source: Expert opinion on drug discovery. 10(9):1025-1032

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100102903452.0x000001&indx=1&recIds=ETOCvdc_100102903452.0x000001

Preclinical discovery and development of maraviroc for the treatment of HIV

Authors: Veljkovic, Nevena, Vucicevic, Jelica, Tassini, Sabrina, Glisic, Sanja, Veljkovic, Veljko, Radi, Marco

Source: Expert opinion on drug discovery. 10(6):671-684

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100102903279.0x000001&indx=1&recIds=ETOCvdc_100102903279.0x000001

The association of V249I and T280M fractalkine receptor haplotypes with disease course of multiple sclerosis

Authors: Stojković, Ljiljana, Djurić, Tamara, Stanković, Aleksandra, Dinčić, Evica, Stančić, Olja, Veljković, Nevena, Alavantić, Dragan, Živković, Maja

Source: In Journal of Neuroimmunology April 2012 245(1-2):87-92

Can natural antibodies to VIP or VIP-like HIV-1 glycoprotein facilitate prevention and supportive treatment of breast cancer?

Authors: Veljkovic, Milena, Branch, Donald R., Dopsaj, Violeta, Veljkovic, Veljko, Veljkovic, Nevena, Glisic, Sanja, Colombatti, Alfonso

Source: In Medical Hypotheses September 2011 77(3):404-408

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

Authors: Perovic, Vladimir, Sumonja, Neven, Gemovic, Branislava, Toska, Eneda, Roberts, Stefan G., Veljkovic, Nevena

Source: Bioinformatics. 33(2):289-291

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100081718188.0x000001&indx=1&recIds=ETOCvdc_100081718188.0x000001

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

Authors: Sencanski, Milan, Glisic, Sanja, Šnajder, Marko, Veljkovic, Nevena, Poklar Ulrih, Nataša, Mavri, Janez, Vrecl, Milka

Source: Scientific reports. 9(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131415550.0x000001&indx=1&recIds=ETOCvdc_100131415550.0x000001

Imidazoline-1 Receptor Ligands as Apoptotic Agents: Pharmacophore Modeling and Virtual Docking Study

Authors: Nikolic, Katarina, Veljkovic, Nevena, Gemovic, Branislava, Srdic-Rajic, Tatjana, Agbaba, Danica

Source: Combinatorial chemistry & high throughput screening. 16(4):298-319

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100083474438.0x000001&indx=1&recIds=ETOCvdc_100083474438.0x000001