@mastersthesis{MTMT:34206953,
	title = {A CFTR kloridcsatorna vizsgálata molekula dinamika szimulációk segítségével},
	url = {https://m2.mtmt.hu/api/publication/34206953},
	author = {Farkas, Bianka Vivien},
	doi = {10.15774/PPKE.ITK.2023.006},
	publisher = {PPKE},
	unique-id = {34206953},
	year = {2023},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864}
}

@article{MTMT:32853643,
	title = {Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1},
	url = {https://m2.mtmt.hu/api/publication/32853643},
	author = {Padányi, Rita and Farkas, Bianka Vivien and Tordai, Hedvig and Kiss, Bálint and Grubmüller, Helmut and Soya, Naoto and Lukács, Gergely L. and Kellermayer, Miklós and Hegedűs, Tamás},
	doi = {10.1016/j.csbj.2022.05.036},
	journal-iso = {CSBJ},
	journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL},
	volume = {20},
	unique-id = {32853643},
	issn = {2001-0370},
	abstract = {Cystic fibrosis (CF) is a frequent genetic disease in Caucasians that is caused by the deletion of F508 (DF508) in the nucleotide binding domain 1 (NBD1) of the CF transmembrane conductance regulator (CFTR). The DF508 compromises the folding energetics of the NBD1, as well as the folding of three other CFTR domains. Combination of FDA approved corrector molecules can efficiently but incompletely rescue the DF508-CFTR folding and stability defect. Thus, new pharmacophores that would reinstate the wildtype-like conformational stability of the DF508-NBD1 would be highly beneficial. The most prominent molecule, 5-bromoindole-3-acetic acid (BIA) that can thermally stabilize the NBD1 has low potency and efficacy. To gain insights into the NBD1 (un)folding dynamics and BIA binding site localization, we combined molecular dynamics (MD) simulations, atomic force spectroscopy (AFM) and hydrogendeuterium exchange (HDX) experiments. We found that the NBD1 a-subdomain with three adjacent strands from the b-subdomain plays an important role in early folding steps, when crucial non-native interactions are formed via residue F508. Our AFM and HDX experiments showed that BIA associates with this a-core region and increases the resistance of the DF508-NBD1 against mechanical unfolding, a phenomenon that could be exploited in future developments of folding correctors. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
	year = {2022},
	eissn = {2001-0370},
	pages = {2587-2599},
	orcid-numbers = {Padányi, Rita/0000-0001-7798-0463; Farkas, Bianka Vivien/0000-0002-0258-6864; Tordai, Hedvig/0000-0002-0875-5569; Kiss, Bálint/0000-0002-1595-0426; Kellermayer, Miklós/0000-0002-5553-6553; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:32612583,
	title = {Ins and outs of AlphaFold2 transmembrane protein structure predictions},
	url = {https://m2.mtmt.hu/api/publication/32612583},
	author = {Hegedűs, Tamás and Geisler, Markus and Lukács, Gergely László and Farkas, Bianka Vivien},
	doi = {10.1007/s00018-021-04112-1},
	journal-iso = {CELL MOL LIFE SCI},
	journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
	volume = {79},
	unique-id = {32612583},
	issn = {1420-682X},
	year = {2022},
	eissn = {1420-9071},
	orcid-numbers = {Hegedűs, Tamás/0000-0002-0331-9629; Geisler, Markus/0000-0002-6641-5810; Lukács, Gergely László/0000-0003-0900-0675; Farkas, Bianka Vivien/0000-0002-0258-6864}
}

@article{MTMT:32499276,
	title = {Effect of F508 deletion on the CFTR NBD1 nanomechanics},
	url = {https://m2.mtmt.hu/api/publication/32499276},
	author = {Farkas, Bianka Vivien},
	journal-iso = {PHD PROC PPKE IT},
	journal = {PHD PROCEEDINGS ANNUAL ISSUES OF THE DOCTORAL SCHOOL FACULTY OF INFORMATION TECHNOLOGY AND BIONICS},
	volume = {16},
	unique-id = {32499276},
	issn = {2064-7271},
	year = {2021},
	pages = {33},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864}
}

@article{MTMT:32499230,
	title = {Mechanical unfolding of the CFTR chloride channel NBD1 domain using force probe simulations},
	url = {https://m2.mtmt.hu/api/publication/32499230},
	author = {Farkas, Bianka Vivien},
	journal-iso = {PHD PROC PPKE IT},
	journal = {PHD PROCEEDINGS ANNUAL ISSUES OF THE DOCTORAL SCHOOL FACULTY OF INFORMATION TECHNOLOGY AND BIONICS},
	volume = {15},
	unique-id = {32499230},
	issn = {2064-7271},
	year = {2020},
	pages = {33},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864}
}

@CONFERENCE{MTMT:31363671,
	title = {Nanomechanics of the CFTR NBD1},
	url = {https://m2.mtmt.hu/api/publication/31363671},
	author = {Farkas, Bianka Vivien and R., Padányi and Tordai, Hedvig and B., Kiss and M., Kellermayer and T., Hegedűs},
	booktitle = {ABC2020 - 8th FEBS Special Meeting},
	unique-id = {31363671},
	year = {2020},
	pages = {77},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864; Tordai, Hedvig/0000-0002-0875-5569}
}

@article{MTMT:31177534,
	title = {Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps},
	url = {https://m2.mtmt.hu/api/publication/31177534},
	author = {Gáspárné Csizmadia, Georgina and Farkas, Bianka Vivien and Katona, E. and Tusnády, Gábor and Hegedűs, Tamás},
	doi = {10.1007/978-1-0716-0270-6_9},
	journal-iso = {METHODS MOL BIOL},
	journal = {METHODS IN MOLECULAR BIOLOGY},
	volume = {2112},
	unique-id = {31177534},
	issn = {1064-3745},
	abstract = {Transmembrane proteins include membrane channels, pores, and receptors and, as such, comprise an important part of the proteome, yet our knowledge about them is much less complete than about soluble, globular proteins. An important aspect of transmembrane protein structure is their exact position within the lipid bilayer, a feature hard to investigate experimentally at the atomic level. Here we describe MemBlob, a novel approach utilizing difference electron density maps obtained by cryo-EM studies of transmembrane proteins. The idea behind is that the nonprotein part of such maps carries information on the exact localization of the membrane mimetics used in the experiment and can be used to extract the positional information of the protein within the membrane. MemBlob uses a structural model of the protein and an experimental electron density map to provide an estimation of the surface residues interacting with the membrane.},
	keywords = {transmembrane region; Cryo-EM map; Lipid interface},
	year = {2020},
	eissn = {1940-6029},
	pages = {123-130},
	orcid-numbers = {Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Farkas, Bianka Vivien/0000-0002-0258-6864; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:30745372,
	title = {MemBlob database and server for identifying transmembrane regions using cryo-EM maps},
	url = {https://m2.mtmt.hu/api/publication/30745372},
	author = {Farkas, Bianka Vivien and Gáspárné Csizmadia, Georgina and Katona, Eszter and Tusnády, Gábor and Hegedűs, Tamás},
	doi = {10.1093/bioinformatics/btz539},
	journal-iso = {BIOINFORMATICS},
	journal = {BIOINFORMATICS},
	volume = {36},
	unique-id = {30745372},
	issn = {1367-4803},
	abstract = {The identification of transmembrane helices in transmembrane proteins is crucial, not only to understand their mechanism of action, but also to develop new therapies. While experimental data on the boundaries of membrane-embedded regions is sparse, this information is present in cryo-electron microscopy (cryo-EM) density maps and it has not been utilized yet for determining membrane regions. We developed a computational pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientation determined by TMDET algorithm of a given protein result in an output defining the residues assigned to the bulk water phase, lipid interface, and the lipid hydrophobic core. Based on this method, we built a database involving published cryo-EM protein structures and a server to be able to compute this data for newly obtained structures.http://memblob.hegelab.org.Supplementary data are available at Bioinformatics online.},
	year = {2020},
	eissn = {1460-2059},
	pages = {2595-2598},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864; Gáspárné Csizmadia, Georgina/0000-0003-4321-9670; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:30745347,
	title = {Discovering the chloride pathway in the CFTR channel},
	url = {https://m2.mtmt.hu/api/publication/30745347},
	author = {Farkas, Bianka Vivien and Tordai, Hedvig and Padányi, Rita and Tordai, Attila and Gera, János and Paragi, Gábor and Hegedűs, Tamás},
	doi = {10.1007/s00018-019-03211-4},
	journal-iso = {CELL MOL LIFE SCI},
	journal = {CELLULAR AND MOLECULAR LIFE SCIENCES},
	volume = {77},
	unique-id = {30745347},
	issn = {1420-682X},
	year = {2020},
	eissn = {1420-9071},
	pages = {765-778},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864; Tordai, Hedvig/0000-0002-0875-5569; Padányi, Rita/0000-0001-7798-0463; Tordai, Attila/0000-0001-6966-1622; Paragi, Gábor/0000-0001-5408-1748; Hegedűs, Tamás/0000-0002-0331-9629}
}

@article{MTMT:32499209,
	title = {Describing the ion passage through the CFTR ion channel},
	url = {https://m2.mtmt.hu/api/publication/32499209},
	author = {Farkas, Bianka Vivien},
	journal-iso = {PHD PROC PPKE IT},
	journal = {PHD PROCEEDINGS ANNUAL ISSUES OF THE DOCTORAL SCHOOL FACULTY OF INFORMATION TECHNOLOGY AND BIONICS},
	volume = {14},
	unique-id = {32499209},
	issn = {2064-7271},
	year = {2019},
	pages = {31},
	orcid-numbers = {Farkas, Bianka Vivien/0000-0002-0258-6864}
}