Employees

Department of Materials Engineering

Assoc. Prof. Daniela Kalafatović

Contact

Email

daniela.kalafatovic@riteh.uniri.hr

More information

Research interests

  • Peptide-based biomaterials
  • Application of machine learning to peptides
  • Peptide nanotechnology

Present appointments

2025 – present: Associate Professor, Faculty of Engineering, University of Rijeka, Croatia

Previous employment

  • 2024 – 2025: Associate Professor, Faculty of Biotechnology and Drug Development, University of Rijeka, Croatia
  • 2021 – 2024: Head of Medicinal Chemistry Division, Faculty of Biotechnology and Drug Development, University of Rijeka, Croatia
  • 2019 – 2024: Assistant Professor, Faculty of Biotechnology and Drug Development, University of Rijeka, Croatia
  • 2016 – 2018: Marie Curie Co-FUND post-doctoral fellow, Institute for research in Biomedicine (IRB) Barcelona, Spain
  • 2015 – 2016: Research Associate, Nanoscience Initiative, Advanced Science Research Center, City University New York, USA

Education

2011 – 2015: PhD Chemistry, University of Strathclyde, UK. Advisor: Prof. Rein V. Ulijn

2004 – 2010: MSc Pharmaceutical Chemistry and Technology, University of Trieste, Italy

Membership

  • Royal Society of Chemistry (RSC)
  • American Chemical Society (ACS)
  • European Peptide Society (EPS)
  • Croatian Chemical Society

Projects

Ongoing:

  1. 2024 – 2028 COST action Searching for Nanostructured or Pore Forming Peptides for Therapy (SNOOPY), funded by The European Cooperation in Science and Technology (Action Chair & Grant Holder Scientific Representative Daniela Kalafatović, grant no. CA23111)
  2. 2024 – 2025 UNIRI project Design of smart peptide-based materials with emerging functions, funded by University of Rijeka (PI Daniela Kalafatovic, grant no. uniri-23-16)
  3. 2024 – 2025 UNIRI project Antiviral peptide-porphyrin conjugates with improved stability and activity against brain-residing viruses, funded by University of Rijeka (PI Toni Todorovski, grant no. uniri-23-188)
  4. 2024 – 2030 HRZZ young researchers’ career development project, funded by Croatian Science foundation (supervisor: Daniela Kalafatović, grant no. DOK-NPOO-2023-10-8638)
  5. 2022 – 2026 HRZZ young researchers’ career development project, funded by Croatian Science foundation (supervisor: Daniela Kalafatović, grant no. DOK-2021-02-3496)
  6. 2020 – 2025 HRZZ installation research project Design of short catalytic peptides and peptide assemblies (DeShPet), funded by Croatian Science foundation (PI Daniela Kalafatovic, grant no. UIP-2019-04-7999)

Past:

  1. 2024 – 2025 UNIRI-INOVA interdisciplinary project Making short peptides drug-like through serum stability improvement (MuPept sho), funded by University of Rijeka (PI Daniela Kalafatovic, grant no. UNIRI-INOVA-3-23-2)
  2. 2024 – 2025 UNIRI-INOVA interdisciplinary project Artificial Intelligence for Gene Expression Prediction (ANTIGEN), funded by University of Rijeka (PI Goran Mauša, grant no. UNIRI-INOVA-3-23-1)
  3. 2022 – 2025 UNIRI CLASS project Environmental Engineering – stud. pilot program of project-oriented interdisciplinary micro-qualification, funded by University of Rijeka (PI Lado Kranjčević)
  4. 2020 – 2023 UNIRI-plus project for new research directions Applying Machine Learning for the Discovery of Peptides with Catalytic Activity, funded by University of Rijeka (PI Goran Mauša, grant no. uniri-pr-tehnic-19-10)
  5. 2020 – 2023 Applied research project A computational model of flow, flooding and pollution dispersion in rivers and coastal marine areas (KLIMOD), funded by European structural and investment funds (PI Lado Kranjčević, team member: Daniela Kalafatović, grant no. KK.05.1.1.02.0017)
  6. 2020 – 2021 UNIRI multidisciplinary Covid-19 project Sars-CoV-2 supramolecular mimetics for discovery of peptides that induce viral entrapment (PI Daniela Kalafatović)
  7. 2016 – 2018 member of the EU commission project as Marie-Curie COFUND post-doctoral fellow (IRB Barcelona, IRBPostPro2.0, grant agreement ID: 600404)

Journal publications

  1. E. Dražić, D. Jelušić, P. Janković Bevandić, G. Mauša, D. Kalafatovic (2025). Using Machine Learning to Fast-Track Peptide Nanomaterial Discovery, ACS Nano, 19 (12), 20295 –20320; https://doi.org/10.1021/acsnano.5c00670
  2. A. Cabezon, E. Otović, D. Kalafatovic, Á. Piñeiro, G. Mauša, R. Garcia Fandino (2025). Unravelling Cyclic Peptide Membrane Permeability Prediction: A Study on Data Augmentation, Architecture Choices, and Representation Schemes, Digital Discovery, 4, 1259-1275; https://doi.org/10.1039/D4DD00375F
  3. M. Njirjak, L. Žužić, M. Babić, P. Janković, E. Otović, D. Kalafatovic, G. Mauša (2024). Reshaping the discovery of self-assembling peptides with generative AI guided by hybrid deep learning, Nature Machine Intelligence, 6, 1487–1500; https://doi.org/10.1038/s42256-024-00928-1
  4. M. Negovetić, E. Otović, D. Kalafatovic, G. Mauša (2024). Efficiently Solving the Curse of Feature-space Dimensionality for Improved Peptide Classification, Digital Discovery, 3, 1182 – 1193; https://doi.org/10.1039/D4DD00079J
  5. P. Janković, D. Kalafatovic (2024). Determining the esterase activity of peptides and peptide assemblies, Methods in Enzymology, 697, 423-433; https://doi.org/10.1016/bs.mie.2024.02.002 
  6. M. Juković, I. Ratkaj, D. Kalafatovic, NJ Bradshaw (2024). Amyloids, amorphous aggregates and assemblies of peptides–Assessing aggregation, Biophysical chemistry, 308, 107202; https://doi.org/10.1016/j.bpc.2024.107202
  7. P. Janković, M. Babić, M. Perčić, AS Pina, D. Kalafatovic (2023). Factors influencing the catalytic activity of metal-dependent histidine-rich peptides: sequence, conformation, stereochemistry, self-assembly or their interplay?, Molecular Systems Design & Engineering, 8 (11), 1371-1380; Hot article; https://doi.org/10.1039/D3ME00117B
  8. G. Mauša, M. Njirjak, E. Otović, D. Kalafatovic (2023). Configurable soft computing-based generative model: The search for catalytic peptides, MRS Advances, pp. 1-7;  https://doi.org/10.1557/s43580-023-00629-8
  9. P. Janković, E. Otović, G. Mauša, D. Kalafatovic (2023). Manually curated dataset of catalytic peptides for ester hydrolysis, Data in Brief, Vol. 48, 109290; https://doi.org/10.1016/j.dib.2023.109290
  10. T. Todorovski, D. Kalafatovic, D. Andreu (2023). Antiviral Peptide-Based Conjugates: State of the Art and Future Perspectives, Pharmaceutics, 15(2), 357; https://doi.org/10.3390/pharmaceutics15020357
  11. M. Babić, P. Janković, S. Marchesan, G. Mauša, D. Kalafatovic (2022). Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs, Journal of Chemical Information and Modeling, Vol. 62 (24), pp. 6398-6410; https://doi.org/10.1021/acs.jcim.2c00977
  12. A.S. Pina, L. Morgado, K.L. Duncan, S. Carvalho, H.F. Carvalho, A.JM. Barbosa, B. de P Mariz, I.P. Moreira, D. Kalafatovic, B.M. Morais Faustino, V. Narang, T. Wang, C.G. Pappas, I. Ferreira, A.C.A Roque, R.V. Ulijn (2022). Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity, Chemical science 13 (1), 210-217; https://doi.org/10.1039/D1SC04420F
  13. L. Grbčić, S. Družeta, G. Mauša, T. Lipić, D. Vukić Lušić, M. Alvir, I. Lučin, A. Sikirica, D. Davidović, V. Travaš, D. Kalafatovic, K. Pikelj, H. Fajković, T. Holjević, L. Kranjčević (2022). Coastal water quality prediction based on machine learning with feature interpretation and spatio-temporal analysis, Environmental Modelling & Software, Vol. 155, 105458; https://doi.org/10.1016/j.envsoft.2022.105458
  14. E. Otović, M. Njirjak, D. Kalafatovic, G. Mauša (2022). Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides, Journal of Chemical Information and Modeling, Vol. 62, 12, pp. 2961–2972; https://doi.org/10.1021/acs.jcim.2c00526
  15. I. Erjavac, D. Kalafatovic, G. Mauša (2022). Coupled encoding methods for antimicrobial peptide prediction: How sensitive is a highly accurate model?, Artificial Intelligence in the Life Sciences, Vol. 2, 100034; https://doi.org/10.1016/j.ailsci.2022.100034
  16. S. Carvalho, D.Q. Peralta Reis, S.V. Pereira, D. Kalafatovic, A.S. Pina (2022). Catalytic peptides: The challenge between simplicity and functionality, Israel Journal of Chemistry, 62 (9-10), e202200029; https://doi.org/10.1002/ijch.202200029
  17. T. Pavlešić, S. Poljak, D. Mišetić Ostojić, I. Lučin, C.A. Reynolds, D. Kalafatovic, L. Saftić Martinović (2022) Phenolic Composition and Antioxidant Activity of Mint (Mentha spp.) Honey, Food Technology and Biotechnology 60 (4); https://doi.org/10.17113/ftb.60.04.22.7703
  18. P. Janković, I. Šantek, A.S. Pina, D. Kalafatovic (2021). Exploiting Peptide Self-Assembly for the Development of Minimalistic Viral Mimetics, Frontiers in Chemistry; 9:723473; https://doi.org/10.3389/fchem.2021.723473
  19. D. Kalafatovic; G. Mauša; D. Rešetar Maslov; E. Giralt (2020). Bottom-Up Design Approach for OBOC Peptide Libraries, Molecules, 25 (15), 1 –15; https://doi.org/10.3390/molecules25153316
  20. J. Son, D. Kalafatovic, B. Yoo, M. Contel, R. V. Ulijn (2019). Customizing MMP-9 responsive peptide nanoparticles: control of morphology and enzyme kinetics through sequence design, ACS Nano, 13 (2), 1555-1562; https://doi.org/10.1021/acsnano.8b07401
  21. D. Kalafatovic; G. Mauša; T. Todorovski; E. Giralt (2019). Algorithm-supported, mass and sequence diversity-oriented random peptide library design, Journal of Cheminformatics, 11:25, 1 – 15, https://doi.org/10.1186/s13321-019-0347-6
  22. S. Gawrzak, L. Rinaldi, S. Gregorio, E. J. Arenas, F. Salvador, J. Urosevic, C. Figueras-Puig, F. Rojo, I. Del Barco Barrantes, M. Cejalvo, J.M. Palafox, M. Guiu, A. Berenguer-Llergo, A. Symeonidi, A. Bellmunt, D. Kalafatovic, A. Arnal-Estapé, E. Fernández, B. Müllauer, R. Groeneveld, K. Slobodnyuk, C. Stephan-Otto Attolini, C. Saura, J. Arribas, J. Cortes, A. Rovira, M. Muñoz, A. Lluch, V. Serra, J. Albanell, A. Prat, A. R. Nebreda, S. A. Benitah, R. R. Gomis (2018) MSK1 regulates luminal cell differentiation and metastatic dormancy in ER+ breast cancer, Nature Cell Biology, 20, 211–221; https://doi.org/10.1038/s41556-017-0021-z
  23. D. Kalafatovic and E. Giralt (2017) Cell Penetrating Peptides: Design strategies beyond primary structure and amphipathicity, Molecules, 22 (11), 1929; https://doi.org/10.3390/molecules22111929
  24. D. Kalafatovic, M. Nobis, J. Son, K. I. Anderson and R. V. Ulijn (2016) MMP-9 triggered self-assembly of doxorubicin nanofiber depots halts tumor growth, Biomaterials, 98, 192-202; https://doi.org/10.1016/j.biomaterials.2016.04.039
  25. D. Kalafatovic, M. Nobis, N. Javid, P. W. J. M. Frederix, K. I. Anderson, B. R. Saunders and R. V. Ulijn (2015) MMP-9 triggered micelle-to-fibre transitions for slow release of doxorubicin, Biomaterials Science 3 (2), 246–249; https://doi.org/10.1039/C4BM00297K
  26. P. W. J. M. Frederix, Y. M. Abul-Haija, G. G. Scott, D. Kalafatovic, C. G. Pappas, N. Javid, N. T. Hunt, R. V. Ulijn and T. Tuttle (2015) Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels, Nature Chemistry, 7 (1), 30–37; https://doi.org/10.1038/nchem.2122
  27. C. G. Pappas, P. W. J. M. Frederix, T. Mutasa, S. Fleming, Y. M. Abul-Haija, S. M. Kelly, A. Gachagan, D. Kalafatovic, J. Trevino, R. V Ulijn, S. Bai (2015) Alignment of Nanostructured Tripeptide Gels by Directional Ultrasonication, Chemical Communications, 51, 8465-68; https://doi.org/10.1039/C5CC02049B

Committees

Awards

  • Invited lecturer presentation award for SB06—Peptide and Protein-Based Materials section at the 2023 MRS Spring Meeting and Exhibit, San Francisco, USA (2023)
  • Poster prize at the Nanoscience NY 2015 conference, New York, USA (2015)
  • Domino Macro Group Young Researcher 2013 award for the second-best oral presentation at the Macro Group Young Researchers Meeting, Nottingham, UK (2013)

Other academic achievements

  • Member of the Editorial board of Journal of Peptide Science (2024 – )
  • Session leader at the Gordon Research Conference GRC “Self-assembly and Supramolecular Chemistry” (2025), Les Diablerets, Switzerland
  • Elected vice chair (2027) and chair (2029) for the GRC “Self-assembly and Supramolecular Chemistry”, Les Diablerets, Switzerland

Oral presentations at international conferences and training schools

  • 3rd Advanced Training Course in Molecular Bioengineering (Porto, Portugal 2025), invited
  • Boulder Peptide Symposium (Boulder, Colorado, USA 2025)
  •  MultiSMART Modelling School (Glasgow, Scotland, UK 2025), invited
  • GRC on Self-Assembly and Supramolecular Chemistry (Les Diablerets, Switzerland 2025), session leader – invited
  • 10th Indian Peptide Symposium (Pune, India 2025), invited
  • Chemical Biology Symposium (CBS-2025, JNCASR, Bengaluru, India 2025), invited
  • NWO Chains (Veldhoven, Netherlands 2024), invited
  • 13th International Symposium on Nano & Supramolecular Chemistry (ISNSC-13, Cagliari, Italy 2024), invited
  • 37th European Peptide Symposium (EPS, Florence, Italy 2024), invited
  • 20th RSC Chemical Biology and Bioorganic Chemistry Firbush Symposium (Firbush, Scotland, UK 2024)
  • Summer Conference of the Croatian Chemical Society Rijeka-Pula 2024, (Rijeka, Croatia 2024), invited
  • 12th Austrian Peptide Symposium (AtPS, Vienna, Austria 2023), invited
  • 60th Japanese Peptide Symposium (JPS, Otsu, Japan 2023)
  • Peptide Chemistry Day (Zagreb, Croatia 2023), invited
  •  28th American Peptide Symposium (APS, Phoenix, USA 2023), flash talk
  • MRS Spring Meeting 2023 (San Francisco, USA 2023), invited (award)
  • 36th European / 12th International Peptide Symposium (EPS, Sitges, Spain 2022)
  • EuroBioHighTech 2022 (Trieste, Italy 2022)
  • 1st Women in Supramolecular Chemistry workshop (Cagliari, Italy 2021)
  • ICT-20@COVID19 (Croatia/online 2020)
  • BioDesign MegaMeeting, Center for Integrative Proteomics Research, Rutgers University (New Jersey, USA 2015)
  • Peptide Materials for Nanotechnology and Biomedicine (Sorrento, Italy 2013)
  • Macro Group Young Researchers Meeting (Nottingham, UK 2013)

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