Publications

@article{nokey,

title = {Factors influencing the catalytic activity of metal-dependent histidine-rich peptides: sequence, conformation, stereochemistry, self-assembly or their interplay?},

author = {Janković, Patrizia; Babić, Marko; Perčić Marko; Pina, Ana S; Kalafatovic, Daniela },

doi = {10.1039/D3ME00117B},

year  = {2023},

date = {2023-09-13},

urldate = {2023-09-13},

journal = {Molecular Systems Design & Engineering},

volume = {8},

issue = {11},

pages = {1371-1380},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Antiviral Peptide-Based Conjugates: State of the Art and Future Perspectives},

author = {Todorovski, Toni; Kalafatovic, Daniela; Andreu, David },

doi = {https://doi.org/10.3390/pharmaceutics15020357},

year  = {2023},

date = {2023-01-20},

journal = {Pharmaceutics},

volume = {15},

issue = {2},

pages = {357},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jankovic2023manually,

title = {Manually curated dataset of catalytic peptides for ester hydrolysis},

author = {Patrizia Janković and Erik Otović and Goran Mauša and Daniela Kalafatovic},

year  = {2023},

date = {2023-01-01},

journal = {Data in Brief},

pages = {109290},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mauvsa2023configurable,

title = {Configurable soft computing-based generative model: The search for catalytic peptides},

author = {Goran Mauša and Marko Njirjak and Erik Otović and Daniela Kalafatovic},

year  = {2023},

date = {2023-01-01},

journal = {MRS Advances},

pages = {1–7},

publisher = {Springer International Publishing Cham},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Erjavac2022,

title = {Coupled encoding methods for antimicrobial peptide prediction: How sensitive is a highly accurate model?},

author = {Ivan Erjavac and Daniela Kalafatovic and Goran Mauša},

doi = {https://doi.org/10.1016/j.ailsci.2022.100034},

year  = {2022},

date = {2022-05-06},

urldate = {2022-05-06},

journal = {Artificial Intelligence in the Life Sciences},

volume = {2},

number = {100034},

pages = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity},

author = {Pina, Ana S. AND Morgado, Leonor AND Duncan, Krystyna L. AND Carvalho, Sara AND Carvalho, Henrique F. AND Barbosa, Arménio J. M. AND de P. Mariz, Beatriz AND Moreira, Inês P. AND Kalafatovic, Daniela AND Morais Faustino, Bruno M. AND Narang, Vishal AND Wang, Tong AND Pappas, Charalampos G. AND Ferreira, Isabel AND Roque, A. Cecília A. AND Ulijn, Rein V. },

doi = {10.1039/D1SC04420F},

year  = {2022},

date = {2022-01-07},

urldate = {2022-01-07},

journal = {Chemical Science },

volume = {13},

pages = {210-217},

abstract = {We demonstrate phage-display screening on self-assembled ligands that enables the identification of oligopeptides that selectively bind dynamic supramolecular targets over their unassembled counterparts. The concept is demonstrated through panning of a phage-display oligopeptide library against supramolecular tyrosine-phosphate ligands using 9-fluorenylmethoxycarbonyl-phenylalanine-tyrosine-phosphate (Fmoc-FpY) micellar aggregates as targets. The 14 selected peptides showed no sequence consensus but were enriched in cationic and proline residues. The lead peptide, KVYFSIPWRVPM-NH2 (P7) was found to bind to the Fmoc-FpY ligand exclusively in its self-assembled state with KD = 74 ± 3 μM. Circular dichroism, NMR and molecular dynamics simulations revealed that the peptide interacts with Fmoc-FpY through the KVYF terminus and this binding event disrupts the assembled structure. In absence of the target micellar aggregate, P7 was further found to dynamically alternate between multiple conformations, with a preferred hairpin-like conformation that was shown to contribute to supramolecular ligand binding. Three identified phages presented appreciable binding, and two showed to catalyze the hydrolysis of a model para-nitro phenol phosphate substrate, with P7 demonstrating conformation-dependent activity with a modest kcat/KM = 4 ± 0.3 × 10−4 M−1 s−1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{grbvcic2022coastal,

title = {Coastal water quality prediction based on machine learning with feature interpretation and spatio-temporal analysis},

author = {Luka Grbčić and Siniša Družeta and Goran Mauša and Tomislav Lipić and Darija Vukić Lušić and Marta Alvir and Ivana Lučin and Ante Sikirica and Davor Davidović and Vanja Travaš and others},

year  = {2022},

date = {2022-01-01},

journal = {Environmental Modelling & Software},

volume = {155},

pages = {105458},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{luvcin2022predictive,

title = {Predictive modeling of microbiological seawater quality in karst region using cascade model},

author = {Ivana Lučin and Siniša Družeta and Goran Mauša and Marta Alvir and Luka Grbčić and Darija Vukić Lušić and Ante Sikirica and Lado Kranjčević},

year  = {2022},

date = {2022-01-01},

journal = {Science of The Total Environment},

volume = {851},

pages = {158009},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{otović2022sequential,

title = {Sequential properties representation scheme for recurrent neural network-based prediction of therapeutic peptides},

author = {Erik Otović and Marko Njirjak and Daniela Kalafatovic and Goran Mauša},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Chemical Information and Modeling},

volume = {62},

number = {12},

pages = {2961–2972},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{babić2022esterase,

title = {Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs},

author = {Marko Babić and Patrizia Janković and Silvia Marchesan and Goran Mauša and Daniela Kalafatovic},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Chemical Information and Modeling},

volume = {62},

number = {24},

pages = {6398–6410},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Intra-domain and cross-domain transfer learning for time series data – How transferable are the features?},

author = {Erik Otović AND Marko Njirjak AND Dario Jozinović AND Goran Mauša AND Alberto Michelini AND Ivan S̆tajduhar},

doi = {https://doi.org/10.1016/j.knosys.2021.107976},

year  = {2021},

date = {2021-12-24},

journal = {Knowledge-Based Systems},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jankovic2021virusmimetics,

title = {Exploiting Peptide Self-Assembly for the Development of Minimalistic Viral Mimetics},

author = {Janković, Patrizia and Šantek, Iva and Pina, Ana Sofia and Kalafatovic, Daniela},

doi = {10.3389/fchem.2021.723473},

year  = {2021},

date = {2021-07-28},

journal = {Frontiers in Chemistry},

volume = {9},

pages = {594},

abstract = {Viruses are natural supramolecular nanostructures that form spontaneously by molecular self-assembly of complex biomolecules. Peptide self-assembly is a versatile tool that allows mimicking viruses by creating their simplified versions through the design of functional, supramolecular materials with modularity, tunability, and responsiveness to chemical and physical stimuli. The main challenge in the design and fabrication of peptide materials is related to the precise control between the peptide sequence and its resulting supramolecular morphology. We provide an overview of existing sequence patterns employed for the development of spherical and fibrillar peptide assemblies that can act as viral mimetics, offering the opportunity to tackle the challenges of viral infections.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kalafatovic2020,

title = {Bottom-Up Design Approach for OBOC Peptide Libraries},

author = {Daniela Kalafatovic and Goran Mauša and Dina Rešetar Maslov and Ernest Giralt},

doi = {https://doi.org/10.3390/molecules25153316},

year  = {2020},

date = {2020-07-22},

urldate = {2020-07-22},

journal = {Molecules},

volume = {25},

number = {15},

pages = {15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{son2019customizing,

title = {Customizing morphology, size, and response kinetics of matrix metalloproteinase-responsive nanostructures by systematic peptide design},

author = {Jiye Son and Daniela Kalafatovic and Mohit Kumar and Barney Yoo and Mike A Cornejo and Mar{'i}a Contel and Rein V Ulijn},

year  = {2019},

date = {2019-01-01},

journal = {ACS nano},

volume = {13},

number = {2},

pages = {1555--1562},

publisher = {ACS Publications},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kalafatovic2019algorithm,

title = {Algorithm-supported, mass and sequence diversity-oriented random peptide library design},

author = {Daniela Kalafatovic and Goran Mauša and Toni Todorovski and Ernest Giralt},

doi = {https://doi.org/10.1186/s13321-019-0347-6},

year  = {2019},

date = {2019-01-01},

journal = {Journal of cheminformatics},

volume = {11},

number = {1},

pages = {25},

publisher = {Springer},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gawrzak2018msk1,

title = {MSK1 regulates luminal cell differentiation and metastatic dormancy in ER+ breast cancer},

author = {Sylwia Gawrzak and Lorenzo Rinaldi and Sara Gregorio and Enrique J Arenas and Fernando Salvador and Jelena Urosevic and Cristina Figueras-Puig and Federico Rojo and Ivan del Barco Barrantes and Juan Miguel Cejalvo and others},

year  = {2018},

date = {2018-01-01},

journal = {Nature cell biology},

volume = {20},

number = {2},

pages = {211},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kalafatovic2017cell,

title = {Cell-penetrating peptides: Design strategies beyond primary structure and amphipathicity},

author = {Daniela Kalafatovic and Ernest Giralt},

year  = {2017},

date = {2017-01-01},

journal = {Molecules},

volume = {22},

number = {11},

pages = {1929},

publisher = {Multidisciplinary Digital Publishing Institute},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mauvsa2017co,

title = {Co-evolutionary multi-population genetic programming for classification in software defect prediction: an empirical case study},

author = {Goran Mauša and Tihana Galinac Grbac},

year  = {2017},

date = {2017-01-01},

journal = {Applied soft computing},

volume = {55},

pages = {331--351},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kalafatovic2016mmp,

title = {MMP-9 triggered self-assembly of doxorubicin nanofiber depots halts tumor growth},

author = {Daniela Kalafatovic and Max Nobis and Jiye Son and Kurt I Anderson and Rein V Ulijn},

doi = {10.1016/j.biomaterials.2016.04.039},

year  = {2016},

date = {2016-01-01},

journal = {Biomaterials},

volume = {98},

pages = {192--202},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mausa2015a,

title = {A Systematic Data Collection Procedure for Software Defect Prediction},

author = {Goran Mauša and Tihana Galinac Grbac and Bojana Dalbelo Bašić},

year  = {2016},

date = {2016-01-01},

journal = {Computer Science and Information Systems},

volume = {13},

pages = {173-197},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{frederix2015exploring,

title = {Exploring the sequence space for (tri-) peptide self-assembly to design and discover new hydrogels},

author = {Pim WJM Frederix and Gary G Scott and Yousef M Abul-Haija and Daniela Kalafatovic and Charalampos G Pappas and Nadeem Javid and Neil T Hunt and Rein V Ulijn and Tell Tuttle},

doi = {https://doi.org/10.1038/nchem.2122},

year  = {2015},

date = {2015-01-01},

journal = {Nature chemistry},

volume = {7},

number = {1},

pages = {30},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kalafatovic2015mmp,

title = {MMP-9 triggered micelle-to-fibre transitions for slow release of doxorubicin},

author = {Daniela Kalafatovic and Max Nobis and Nadeem Javid and Pim WJM Frederix and Kurt I Anderson and Brian R Saunders and Rein V Ulijn},

year  = {2015},

date = {2015-01-01},

journal = {Biomaterials science},

volume = {3},

number = {2},

pages = {246--249},

publisher = {Royal Society of Chemistry},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pappas2015alignment,

title = {Alignment of nanostructured tripeptide gels by directional ultrasonication},

author = {Charalampos G Pappas and Pim WJM Frederix and Tapiwa Mutasa and Scott Fleming and Yousef M Abul-Haija and Sharon M Kelly and Anthony Gachagan and Daniela Kalafatovic and Jacob Trevino and Rein V Ulijn and others},

year  = {2015},

date = {2015-01-01},

journal = {Chemical communications},

volume = {51},

number = {40},

pages = {8465--8468},

publisher = {Royal Society of Chemistry},

keywords = {},

pubstate = {published},

tppubtype = {article}

}