Mateusz Banach, PhD

Received PhD in technical sciences (discipline: Computer Science) from Institute of Fundamental Technological Research – Polish Academy of Sciences in Warsaw in 2018. Received MSc in Computer Science from Faculty of Physics, Astronomy and Applied Computer Science – Jagiellonian University in Krakow in 2009. Currently employed as assistant professor.

Contact form and class schedule

https://www.usosweb.uj.edu.pl/kontroler.php?_action=katalog2/osoby/pokazOsobe&os_id=2492

To see the e-mail address, choose “show email address” on the right of the above website.

Conducted courses

  • Telemedycyna z elementami symulacji medycznej
  • Informatyka i Statystyka Medyczna 2/2
  • Informatyka – fakultet
  • Telemedicine with Elements of Medical Simulation
  • Computer science and medical statistics
  • Medical Informatics including biostatistics 2/2
  • Biochemistry with Elements of Chemistry

Research projects

  • 2018 – 2019: bilateral cooperation between Jagiellonian University – Medical College and Sorbonne Université (previously Université Pierre-et-Marie-Curie / Paris VI)  under PHC Polonium grant no. 405111TL
  • 2012 – 2013: bilateral cooperation between Jagiellonian University – Medical College and Sorbonne Université (previously Université Pierre-et-Marie-Curie / Paris VI)  under PHC Polonium grant no. 27748NE

Publication list (selected titles)

Complete and up to date list of all publications is available at the website of Medical Library.

Articles
  1. Banach, M., Fabian, P., Stapor, K., Konieczny, L., Ptak-Kaczor, M., & Roterman, I. (2020). The Status of Edge Strands in Ferredoxin-Like Fold. Symmetry, Vol. 12(nr 6). https://doi.org/10.3390/sym12061032
  2. Banach, M., Fabian, P., Stapor, K., Konieczny, L., & Roterman, I. (2020). Structure of the Hydrophobic Core Determines the 3D Protein Structure-Verification by Single Mutation Proteins. Biomolecules, Vol. 10(nr 5). https://doi.org/10.3390/biom10050767
  3. Banach, M., Stapor, K., Konieczny, L., Fabian, P., & Roterman, I. (2020). Downhill, Ultrafast and Fast Folding Proteins Revised. International Journal of Molecular Sciences, Vol. 21(nr 20). https://doi.org/10.3390/ijms21207632
  4. Dułak, D., Gadzała, M., Banach, M., Konieczny, L., & Roterman, I. (2020). Alternative Structures of α-Synuclein. Molecules, Vol. 25(nr 3). https://doi.org/10.3390/molecules25030600
  5. Fabian, P., Banach, M., Stapor, K., Konieczny, L., Ptak-Kaczor, M., & Roterman, I. (2020). The Structure of Amyloid Versus the Structure of Globular Proteins. International Journal of Molecular Sciences, Vol. 21(nr 13). https://doi.org/10.3390/ijms21134683
  6. Fabian, P., Stapor, K., Banach, M., Ptak-Kaczor, M., Konieczny, L., & Roterman, I. (2020). Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy. Symmetry, Vol. 12(nr 2). https://doi.org/10.3390/sym12020273
  7. Banach, M., Konieczny, L., & Roterman, I. (2019). Symmetry and Dissymmetry in Protein Structure-System-Coding Its Biological Specificity. Symmetry, Vol. 11(nr 10), 1215. https://doi.org/10.3390/sym11101215
  8. Banach, M., Konieczny, L., & Roterman, I. (2019). The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. Molecules, Vol. 24(nr 23), 4395. https://doi.org/10.3390/molecules24234395
  9. Fabian, P., Stapor, K., Banach, M., Ptak-Kaczor, M., Konieczny, L., & Roterman, I. (2019). Different Synergy in Amyloids and Biologically Active Forms of Proteins. International Journal of Molecular Sciences, Vol. 20(nr 18), 4436. https://doi.org/10.3390/ijms20184436
  10. Gadzała, M., Dułak, D., Kalinowska, B., Baster, Z., Bryliński, M., Konieczny, L., Banach, M., & Roterman, I. (2019). The aqueous environment as an active participant in the protein folding process. Journal of Molecular Graphics & Modelling, Vol. 87, s. 227-239. https://doi.org/10.1016/j.jmgm.2018.12.008
  11. Ptak-Kaczor, M., Banach, M., Konieczny, L., & Roterman, I. (2019). Internal force field in selected proteins. Acta Biochimica Polonica, Vol. 66(nr 4, Part I), s. 451-458. https://doi.org/10.18388/abp.2019_2865
  12. Roterman, I., Dułak, D., Gadzała, M., Banach, M., & Konieczny, L. (2019). Structural analysis of the Aβ(1142) amyloid fibril based on hydrophobicity distribution. Journal of Computer-Aided Molecular Design, Vol. 33(nr 7), s. 665-675. https://doi.org/10.1007/s10822-019-00209-9
  13. Banach, M., Konieczny, L., & Roterman, I. (2018). Why do antifreeze proteins require a solenoid? Biochimie, Vol. 144, s. 74-84. https://doi.org/10.1016/j.biochi.2017.10.011
  14. Dułak, D., Banach, M., Gadzała, M., Konieczny, L., & Roterman, I. (2018). Structural analysis of the Aβ(15-40) amyloid fibril based on hydrophobicity distribution. Acta Biochimica Polonica, Vol. 65(nr 4), s. 595-604. https://doi.org/10.18388/abp.2018_2647
  15. Dułak, D., Gadzała, M., Banach, M., Ptak, M., Wiśniowski, Z., Konieczny, L., & Roterman, I. (2018). Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model. International Journal of Molecular Sciences, Vol. 19(nr 10 art. no. 2910), s. 1-29. https://doi.org/10.3390/ijms19102910
  16. Gadzała, M., Kalinowska, B., Banach, M., Konieczny, L., & Roterman, I. (2017). Determining protein similarity by comparing hydrophobic core structure. Heliyon, Vol. 3(nr 2 art. no. e00235), s. 1-32. https://doi.org/10.1016/j.heliyon.2017.e00235
  17. Kalinowska, B., Banach, M., Wiśniowski, Z., Konieczny, L., & Roterman, I. (2017). Is the hydrophobic core a universal structural element in proteins? Journal of Molecular Modeling, Vol. 23(nr 7 art. no. 203), s. 1-16. https://doi.org/10.1007/s00894-017-3367-z
  18. Roterman, I., Banach, M., & Konieczny, L. (2017). Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. Entropy, Vol. 19(nr 4 art. no. 167), s. 1-19. https://doi.org/10.3390/e19040167
  19. Roterman, I., Banach, M., & Konieczny, L. (2017). Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. Pharmaceuticals, Vol. 10(nr 4 art. nr 89), s. 1-15. https://doi.org/10.3390/ph10040089
  20. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2016). Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes-An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins. Entropy, Vol. 18(nr 3 art. no. 67), s. 1-21. https://doi.org/10.3390/e18030067
  21. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2016). Sequence-to-Structure Relation in Proteins-Amyloidogenic Proteins with Chameleon Sequences. Journal of Proteomics and Bioinformatics, Vol. 9(nr 11), s. 264-275. https://doi.org/10.4172/jpb.1000415
  22. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2016). Structural Role of Hydrophobic Core in Proteins-Selected Examples. Journal of Proteomics and Bioinformatics, Vol. 9(nr 11), s. 276-286. https://doi.org/10.4172/jpb.1000416
  23. Dygut, J., Kalinowska, B., Banach, M., Piwowar, M., Konieczny, L., & Roterman, I. (2016). Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. International Journal of Molecular Sciences, Vol. 17(nr 10 art. no. E1741), s. 1-21. https://doi.org/10.3390/ijms17101741
  24. Roterman, I., Banach, M., Kalinowska, B., & Konieczny, L. (2016). Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis. Entropy, Vol. 18(nr 10 art. no. 351), s. 1-31. https://doi.org/10.3390/e18100351
  25. Banach, M., Prudhomme, N., Carpentier, M., Duprat, E., Papandreou, N., Kalinowska, B., Chomilier, J., & Roterman, I. (2015). Contribution to the prediction of the fold code: Application to immunoglobulin and flavodoxin cases. PLoS One, Vol. 10(nr 4 art. no. e0125098), s. 1-26. https://doi.org/10.1371/journal.pone.0125098
  26. Kalinowska, B., Banach, M., Konieczny, L., & Roterman, I. (2015). Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy, Vol. 17(nr 3), s. 1477-1507. https://doi.org/10.3390/e17031477
  27. Banach, M., Konieczny, L., & Roterman, I. (2014). The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function. Journal of Theoretical Biology, Vol. 351, s. 6-17. https://doi.org/10.1016/j.jtbi.2014.05.007
  28. Kalinowska, B., Banach, M., Konieczny, L., Marchewka, D., & Roterman, I. (2014). Intrinsically disordered proteins-relation to general model expressing the active role of the water environment. Advances in Protein Chemistry and Structural Biology, Vol. 94, s. 315-346. https://doi.org/10.1016/B978-0-12-800168-4.00008-1
  29. Piwowar, M., Banach, M., Konieczny, L., & Roterman, I. (2014). Hydrophobic core formation in protein complex of cathepsin. Journal of Biomolecular Structure & Dynamics, Vol. 32(nr 7), s. 1023-1032. https://doi.org/10.1080/07391102.2013.801784
  30. Piwowar, M., Banach, M., Konieczny, L., & Roterman, I. (2013). Structural role of exon-coded fragment of polypeptide chains in selected enzymes. Journal of Theoretical Biology, Vol. 337, s. 15-23. https://doi.org/10.1016/j.jtbi.2013.07.016
  31. Banach, M., Prymula, K., Jurkowski, W., Konieczny, L., & Roterman, I. (2012). Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants. Journal of Molecular Modeling, Vol. 18(nr 1), s. 229-237. https://doi.org/10.1007/s00894-011-1033-4
  32. Roterman, I., Konieczny, L., Banach, M., & Jurkowski, W. (2011). Intermediates in the protein folding process: A computational model. International Journal of Molecular Sciences, Vol. 12(nr 8), s. 4850-4860. https://doi.org/10.3390/ijms11084850
  33. Banach, M., Stąpor, K., & Roterman, I. (2009). Chaperonin structure—The large multi-subunit protein complex. International Journal of Molecular Sciences, Vol. 10(nr 3), s. 844-861. https://doi.org/10.3390/ijms10030844
Chapters in collections
  1. Banach, M., Konieczny, L., & Roterman, I. (2020). Anti-amyloid drug design. In From Globular Proteins to Amyloids. (p. s. 215-231). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00019-1
  2. Banach, M., Konieczny, L., & Roterman, I. (2020). Composite structures. In From Globular Proteins to Amyloids. (p. s. 117-133). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00011-7
  3. Banach, M., Konieczny, L., & Roterman, I. (2020). Ligand binding cavity encoded as a local hydrophobicity deficiency. In From Globular Proteins to Amyloids. (p. s. 91-93). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00009-9
  4. Banach, M., Konieczny, L., & Roterman, I. (2020). Local discordance. In From Globular Proteins to Amyloids. (p. s. 69). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00006-3
  5. Banach, M., Konieczny, L., & Roterman, I. (2020). Protein-protein interaction encoded as an exposure of hydrophobic residues on the surface. In From Globular Proteins to Amyloids. (p. s. 79-89). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00008-7
  6. Banach, M., Konieczny, L., & Roterman, I. (2020). Proteins structured as spherical micelles. In From Globular Proteins to Amyloids. (p. s. 55-68). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00005-1
  7. Banach, M., Konieczny, L., & Roterman, I. (2020). The active site in a single-chain enzyme. In From Globular Proteins to Amyloids. (p. s. 71-78). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00007-5
  8. Banach, M., Konieczny, L., & Roterman, I. (2020). The hypothetical amyloid transformation of transthyretin. In From Globular Proteins to Amyloids. (p. s. 233-240). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00020-8
  9. Banach, M., & Roterman, I. (2020). Amyloid as a ribbon-like micelle. In From Globular Proteins to Amyloids. (p. s. 177-191). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00016-6
  10. Banach, M., & Roterman, I. (2020). Amyloids identification based on fuzzy oil drop model. In From Globular Proteins to Amyloids. (p. s. 173-175). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00015-4
  11. Banach, M., & Roterman, I. (2020). Complexes AΒ(142) polypeptide with non-protein molecules. In From Globular Proteins to Amyloids. (p. s. 137-156). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00013-0
  12. Banach, M., & Roterman, I. (2020). Non-amyloid structure of the AΒ(142) polypeptide in presence of a permanent chaperone. In From Globular Proteins to Amyloids. (p. s. 135-136). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00012-9
  13. Banach, M., & Roterman, I. (2020). Solenoid—An amyloid under control. In From Globular Proteins to Amyloids. (p. s. 95-115). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00010-5
  14. Banach, M., & Roterman, I. (2020). Specificity of amino acid sequence and its role in secondary and supersecondary structure generation. In From Globular Proteins to Amyloids. (p. s. 207-214). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00018-X
  15. Banach, M., & Roterman, I. (2020). Structure of selected fragments of AΒ(142) in complex with other proteins. In From Globular Proteins to Amyloids. (p. s. 157-172). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00014-2
  16. Dułak, D., Gadzała, M., Banach, M., & Roterman, I. (2020). Analysis of alternative conformations of the AΒ(140) amyloid protein. In From Globular Proteins to Amyloids. (p. s. 193-206). Elsevier. https://doi.org/10.1016/B978-0-08-102981-7.00017-8
  17. Banach, M., Konieczny, L., & Roterman, I. (2019). Fuzzy Oil Drop Model Application-From Globular Proteins to Amyloids. In Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. From Bioinformatics to Molecular Quantum Mechanics. (p. s. 639-658). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-319-95843-9_19
  18. Banach, M., Konieczny, L., & Roterman, I. (2019). Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores. In Protein supersecondary structures. Methods and Protocols. (p. s. 347-378). Springer Science + Business Media. https://doi.org/10.1007/978-1-4939-9161-7_19
  19. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2018). Possible mechanism of amyloidogenesis of V domains. In Self-Assembled Molecules New Kind of Protein Ligands: Supramolecular Ligands. (p. s. 77-100). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-319-65639-7_5
  20. Roterman, I., Konieczny, L., Banach, M., Marchewka, D., Kalinowska, B., Baster, Z., Tomanek, M., & Piwowar, M. (2014). Simulation of the protein folding process. In Computational methods to study the structure and dynamics of biomolecules and biomolecular processes: From bioinformatics to molecular quantum mechanics. (p. s. 599-638). Springer. https://doi.org/10.1007/978-3-642-28554-7_18
  21. Alejster, P., Banach, M., Jurkowski, W., Marchewka, D., & Roterman-Konieczna, I. (2013). Comparative analysis of techniques oriented on the recognition of ligand binding area in proteins. In Identification of ligand binding site and protein-protein interaction area. (p. s. 55-86). Springer. https://doi.org/10.1007/978-94-007-5285-6_4
  22. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2013). Can the structure of the hydrophobic core determine the complexation site? In Identification of ligand binding site and protein-protein interaction area. (p. s. 41-54). Springer. https://doi.org/10.1007/978-94-007-5285-6_3
  23. Marchewka, D., Jurkowski, W., Banach, M., & Roterman-Konieczna, I. (2013). Prediction of protein-protein binding interfaces. In Identification of ligand binding site and protein-protein interaction area. (p. s. 105-134). Springer. https://doi.org/10.1007/978-94-007-5285-6_6
  24. Wiśniowski, Z., Banach, M., & Roterman, I. (2013). Antifreeze compounds to allow survival at temperatures below 0 C deg. In Manufacture Engineering, Quality and Production System II. (p. s. 32-38). Trans Tech Publications. https://doi.org/10.4028/www.scientific.net/AMR.711.32
  25. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Ligand-binding recognition. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 79-93). Woodhead Pub.
  26. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). The late-stage intermediate. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 21-37). Woodhead Pub.
  27. Banach, M., Konieczny, L., & Roterman-Konieczna, I. (2012). Use of the fuzzy oil drop model to identify the complexation area in protein homodimers. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 95-122). Woodhead Pub.
  28. Banach, M., Marchewka, D., Piwowar, M., & Roterman-Konieczna, I. (2012). The divergence entropy characterizing the internal force field in proteins. In Protein folding in silico: Protein folding versus protein structure prediction. (p. s. 55-77). Woodhead Pub.
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