@article{MTMT:34173459,
	title = {The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method},
	url = {https://m2.mtmt.hu/api/publication/34173459},
	author = {Cserző, Miklós and Eisenhaber, Birgit and Eisenhaber, Frank and Magyar, Csaba and Simon, István},
	doi = {10.3390/ijms241814016},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {34173459},
	issn = {1661-6596},
	abstract = {The dense alignment surface (DAS) transmembrane (TM) prediction method was first published more than 25 years ago. DAS was the one of the earliest tools to discriminate TM proteins from globular ones and to predict the sequence positions of TM helices in proteins with high accuracy from their amino acid sequence alone. The algorithmic improvements that followed in 2002 (DAS-TMfilter) made it one of the best performing tools among those relying on local sequence information for TM prediction. Since then, many more experimental data about membrane proteins (including thousands of 3D structures of membrane proteins) have accumulated but there has been no significant improvement concerning performance in the area of TM helix prediction tools. Here, we report a new implementation of the DAS-TMfilter prediction web server. We reevaluated the performance of the method using a five-times-larger, updated test dataset. We found that the method performs at essentially the same accuracy as the original even without any change to the parametrization of the program despite the much larger dataset. Thus, the approach captures the physico-chemistry of TM helices well, essentially solving this scientific problem.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Cserző, Miklós/0000-0002-9425-4487; Eisenhaber, Birgit/0000-0002-2910-7384; Eisenhaber, Frank/0000-0002-9599-5420; Magyar, Csaba/0000-0002-5023-6180}
}

@book{MTMT:33770993,
	title = {Frontiers in Protein Structure Research},
	url = {https://m2.mtmt.hu/api/publication/33770993},
	isbn = {9783036567808},
	doi = {10.3390/books978-3-0365-6780-8},
	editor = {Simon, István and Magyar, Csaba},
	publisher = {MDPI AG},
	unique-id = {33770993},
	year = {2023},
	orcid-numbers = {Magyar, Csaba/0000-0002-5023-6180}
}

@article{MTMT:33585703,
	title = {Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins},
	url = {https://m2.mtmt.hu/api/publication/33585703},
	author = {Magyar, Csaba and Németh, Zoltán Bálint and Cserző, Miklós and Simon, István},
	doi = {10.3390/ijms24021790},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {33585703},
	issn = {1661-6596},
	abstract = {Mutual synergistic folding (MSF) proteins belong to a recently emerged subclass of disordered proteins, which are disordered in their monomeric forms but become ordered in their oligomeric forms. They can be identified by experimental methods following their unfolding, which happens in a single-step cooperative process, without the presence of stable monomeric intermediates. Only a limited number of experimentally validated MSF proteins are accessible. The amino acid composition of MSF proteins shows high similarity to globular ordered proteins, rather than to disordered ones. However, they have some special structural features, which makes it possible to distinguish them from globular proteins. Even in the possession of their oligomeric three-dimensional structure, classification can only be performed based on unfolding experiments, which are frequently absent. In this work, we demonstrate a simple protocol using molecular dynamics simulations, which is able to indicate that a protein structure belongs to the MSF subclass. The presumption of the known atomic resolution quaternary structure is an obvious limitation of the method, and because of its high computational time requirements, it is not suitable for screening large databases; still, it is a valuable in silico tool for identification of MSF proteins.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Magyar, Csaba/0000-0002-5023-6180; Németh, Zoltán Bálint/0000-0003-0151-4647; Cserző, Miklós/0000-0002-9425-4487}
}

@article{MTMT:32782154,
	title = {Assortment of Frontiers in Protein Science},
	url = {https://m2.mtmt.hu/api/publication/32782154},
	author = {Simon, István and Magyar, Csaba},
	doi = {10.3390/ijms23073685},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {32782154},
	issn = {1661-6596},
	year = {2022},
	eissn = {1422-0067},
	orcid-numbers = {Magyar, Csaba/0000-0002-5023-6180}
}

@article{MTMT:32552670,
	title = {Origin of increased solvent accessibility of peptide bonds in mutual synergetic folding proteins},
	url = {https://m2.mtmt.hu/api/publication/32552670},
	author = {Magyar, Csaba and Mentes, Anikó and Cserző, Miklós and Simon, István},
	doi = {10.3390/ijms222413404},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {22},
	unique-id = {32552670},
	issn = {1661-6596},
	year = {2021},
	eissn = {1422-0067},
	orcid-numbers = {Magyar, Csaba/0000-0002-5023-6180; Cserző, Miklós/0000-0002-9425-4487}
}

@book{MTMT:31599381,
	title = {Functionally Relevant Macromolecular Interactions of Disordered Proteins},
	url = {https://m2.mtmt.hu/api/publication/31599381},
	isbn = {9783039365227},
	doi = {10.3390/books978-3-03936-522-7},
	editor = {Simon, István},
	publisher = {MDPI AG},
	unique-id = {31599381},
	year = {2020}
}

@article{MTMT:31127720,
	title = {Macromolecular Interactions of Disordered Proteins},
	url = {https://m2.mtmt.hu/api/publication/31127720},
	author = {Simon, István},
	doi = {10.3390/ijms21020504},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {21},
	unique-id = {31127720},
	issn = {1661-6596},
	year = {2020},
	eissn = {1422-0067}
}

@article{MTMT:30875480,
	title = {Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding},
	url = {https://m2.mtmt.hu/api/publication/30875480},
	author = {Mészáros, Bálint and Dobson, László and Fichó, Erzsébet and Simon, István},
	doi = {10.3390/ijms20215460},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {20},
	unique-id = {30875480},
	issn = {1661-6596},
	year = {2019},
	eissn = {1422-0067},
	orcid-numbers = {Fichó, Erzsébet/0000-0002-3965-8438}
}

@article{MTMT:30852006,
	title = {Analysis of Heterodimeric “Mutual Synergistic Folding”-Complexes},
	url = {https://m2.mtmt.hu/api/publication/30852006},
	author = {Mentes, Anikó and Magyar, Csaba and Fichó, Erzsébet and Simon, István},
	doi = {10.3390/ijms20205136},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {20},
	unique-id = {30852006},
	issn = {1661-6596},
	year = {2019},
	eissn = {1422-0067},
	orcid-numbers = {Magyar, Csaba/0000-0002-5023-6180; Fichó, Erzsébet/0000-0002-3965-8438}
}

@article{MTMT:30846550,
	title = {How folding and binding intertwine during protein complex formation provides an additional layer of functional regulation},
	url = {https://m2.mtmt.hu/api/publication/30846550},
	author = {Dobson, László and Fichó, Erzsébet and Tusnády, Gábor and Simon, István and Dosztányi, Zsuzsanna and Mészáros, Bálint},
	journal-iso = {FEBS OPEN BIO},
	journal = {FEBS OPEN BIO},
	volume = {9},
	unique-id = {30846550},
	issn = {2211-5463},
	year = {2019},
	eissn = {2211-5463},
	pages = {265-265},
	orcid-numbers = {Fichó, Erzsébet/0000-0002-3965-8438; Dosztányi, Zsuzsanna/0000-0002-3624-5937}
}