Zakład Bioinformatyki i Telemedycyny

dr Mateusz Banach

Doktor nauk technicznych – dziedzina: Informatyka, stopień naukowy nadany przez Instytut Podstawowych Problemów Techniki Polskiej Akademii Nauk w Warszawie w 2018 r. Tytuł zawodowy magistra (kierunek: Informatyka, specjalność: Informatyka Stosowana) uzyskał na Wydziale Fizyki, Astronomii i Informatyki Stosowanej Uniwersytetu Jagiellońskiego w Krakowie w 2009 r. Obecnie pracuje na stanowisku adiunkta. Członek Polskiego Towarzystwa Informatycznego (obecnie Oddziału Białostockiego) od 2016 r.

https://fod.cm-uj.krakow.pl

Dane kontaktowe

https://www.usosweb.uj.edu.pl/kontroler.php?_action=katalog2/osoby/pokazOsobe&os_id=2492
(aby zobaczyć adres e-mail, wybierz „pokaż adres email” po prawej stronie powyższej witryny)

Odnośniki

Zainteresowania

bioinformatyka, geometria obliczeniowa, informatyka, analiza danych, wizualizacja danych, hydrofobowość, optymalizacja, zwijanie białek, oddziaływania białko-białko, programowanie w pythonie, usługi sieciowe i bazy danych

Prowadzone zajęcia dydaktyczne

  • Telemedycyna z elementami symulacji medycznej (Wydział Lekarski, kierunek lekarski, II rok)
  • Informatyka i Statystyka Medyczna 2/2 (Wydział Lekarski, kierunek lekarsko-dentystyczny, III rok)
  • Telemedicine with Elements of Medical Simulation (Szkoła Medyczna dla Obcokrajowców, kierunek lekarski, II rok)
  • Computer science and medical statistics 1/2 (Szkoła Medyczna dla Obcokrajowców, kierunek lekarsko-dentystyczny, I rok)
  • Computer science and medical statistics 2/2 (Szkoła Medyczna dla Obcokrajowców, kierunek lekarsko-dentystyczny, III rok)
  • Biochemistry with Elements of Chemistry (Szkoła Medyczna dla Obcokrajowców, kierunek lekarski, I rok)

Udział w projektach badawczych

  • 2018 – 2019: współpraca bilateralna pomiędzy Uniwersytetem Jagiellońskim – Collegium Medicum a Sorbonne Université (dawniej Université Pierre-et-Marie-Curie / Paris VI) w ramach grantu PHC Polonium nr 405111TL
  • 2012 – 2013: współpraca bilateralna pomiędzy Uniwersytetem Jagiellońskim – Collegium Medicum a Sorbonne Université (dawniej Université Pierre-et-Marie-Curie / Paris VI) w ramach grantu PHC Polonium nr 27748NE

Działalność w środowisku naukowym

Publikacje w czasopismach

  1. Banach, M. (2023). Structural Outlier Detection and Zernike–Canterakis Moments for Molecular Surface Meshes—Fast Implementation in Python. Molecules, 29(1), 52. https://doi.org/10.3390/molecules29010052
  2. Banach M. (2023) Improved Assessment of Globularity of Protein Structures and the Ellipsoid Profile of the Biological Assemblies from the PDB. Biomolecules, 13(2), 385. https://doi.org/10.3390/biom13020385
  3. Banach M. (2022) Symmetrization in the Calculation Pipeline of Gauss Function-Based Modeling of Hydrophobicity in Protein Structures. Symmetry, 14(9), 1876. https://doi.org/10.3390/sym14091876
  4. Banach M. (2021) Assessment of Globularity of Protein Structures via Minimum Volume Ellipsoids and Voxel-Based Atom Representation. Crystals, 11(12), 1539. https://doi.org/10.3390/cryst11121539
  5. Banach, M., Chomilier, J., & Roterman, I. (2021). Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases. Applied Sciences, 11(18), 8514. https://doi.org/10.3390/app11188514
  6. Ptak-Kaczor, M., Banach, M., Stapor, K., Fabian, P., Konieczny, L., & Roterman, I. (2021). Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution. International Journal of Molecular Sciences, 22(9), 5002. https://doi.org/10.3390/ijms22095002
  7. Banach, M., Stapor, K., Fabian, P., Konieczny, L., & Roterman, I. (2021). Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin. Entropy, 23(4), 458. https://doi.org/10.3390/e23040458
  8. Ptak-Kaczor, M., Kwiecińska, K., Korchowiec, J., Chłopaś, K., Banach, M., Roterman, I., & Anna, J. (2021). Structure and Location of Protein Sites Binding Self-Associated Congo Red Molecules with Intercalated Drugs as Compact Ligands—Theoretical Studies. Biomolecules, 11(4), 501. https://doi.org/10.3390/biom11040501
  9. Roterman, I., Stapor, K., Fabian, P., Konieczny, L., & Banach, M. (2021). Model of Environmental Membrane Field for Transmembrane Proteins. International Journal of Molecular Sciences, 22(7), 3619. https://doi.org/10.3390/ijms22073619
  10. Banach, M., Stapor, K., Konieczny, L., Fabian, P., & Roterman, I. (2020). Downhill, Ultrafast and Fast Folding Proteins Revised. International Journal of Molecular Sciences, 21(20), 7632. https://doi.org/10.3390/ijms21207632
  11. 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, 21(13), 4683. https://doi.org/10.3390/ijms21134683
  12. Banach, M., Fabian, P., Stapor, K., Konieczny, L., Ptak-Kaczor, M., & Roterman, I. (2020). The Status of Edge Strands in Ferredoxin-Like Fold. Symmetry, 12(6), 1032. https://doi.org/10.3390/sym12061032
  13. Banach, M., Fabian, P., Stapor, K., Konieczny, L., & Roterman, and I. (2020). Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins. Biomolecules, 10(5), 767. https://doi.org/10.3390/biom10050767
  14. 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, 12(2), 273. https://doi.org/10.3390/sym12020273
  15. Dułak, D., Gadzała, M., Banach, M., Konieczny, L., & Roterman, I. (2020). Alternative Structures of α-Synuclein. Molecules, 25(3), 600. https://doi.org/10.3390/molecules25030600
  16. Banach, M., Konieczny, L., & Roterman, I. (2019). The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. Molecules, 24(23), 4395. https://doi.org/10.3390/molecules24234395
  17. Ptak-Kaczor, M., Banach, M., Konieczny, L., & Roterman, I. (2019). Internal force field in selected proteins. Acta Biochimica Polonica, 66(4), 451–458. https://doi.org/10.18388/abp.2019_2865
  18. Banach, M., Konieczny, L., & Roterman, I. (2019). Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity. Symmetry, 11(10), 1215. https://doi.org/10.3390/sym11101215
  19. 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, 20(18), 4436. https://doi.org/10.3390/ijms20184436
  20. Roterman, I., Dułak, D., Gadzała, M., Banach, M., & Konieczny, L. (2019). Structural analysis of the Aβ(11–42) amyloid fibril based on hydrophobicity distribution. Journal of Computer-Aided Molecular Design, 33(7), 665–675. https://doi.org/10.1007/s10822-019-00209-9
  21. 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 and Modelling, 87, 227–239. https://doi.org/10.1016/j.jmgm.2018.12.008
  22. 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, 65(4), 595–604. https://doi.org/10.18388/abp.2018_2647
  23. 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, 19(10), 2910. https://doi.org/10.3390/ijms19102910
  24. Banach, M., Konieczny, L., & Roterman, I. (2018). Why do antifreeze proteins require a solenoid? Biochimie, 144, 74–84. https://doi.org/10.1016/j.biochi.2017.10.011
  25. Roterman, I., Banach, M., & Konieczny, L. (2017). Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. Pharmaceuticals, 10(4), 89. https://doi.org/10.3390/ph10040089
  26. 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, 23(7), 205. https://doi.org/10.1007/s00894-017-3367-z
  27. Roterman, I., Banach, M., & Konieczny, L. (2017). Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. Entropy, 19(4), 167. https://doi.org/10.3390/e19040167
  28. Gadzała, M., Kalinowska, B., Banach, M., Konieczny, L., & Roterman, I. (2017). Determining protein similarity by comparing hydrophobic core structure. Heliyon, 3(2), e00235. https://doi.org/10.1016/j.heliyon.2017.e00235
  29. 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, 17(10), 1741. https://doi.org/10.3390/ijms17101741
  30. 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, 18(10), 351. https://doi.org/10.3390/e18100351
  31. 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, 18(3), 67. https://doi.org/10.3390/e18030067
  32. 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, 10(4), e0125098. https://doi.org/10.1371/journal.pone.0125098
  33. 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, 17(3), 1477–1507. https://doi.org/10.3390/e17031477
  34. 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, 359, 6–17. https://doi.org/10.1016/j.jtbi.2014.05.007
  35. Piwowar, M., Banach, M., Konieczny, L., & Roterman, I. (2014). Hydrophobic core formation in protein complex of cathepsin. Journal of Biomolecular Structure and Dynamics, 32(7), 1023–1032. https://doi.org/10.1080/07391102.2013.801784
  36. Banach, M., Roterman, I., Prudhomme, N., & Chomilier, J. (2013). Hydrophobic core in domains of immunoglobulin-like fold. Journal of Biomolecular Structure and Dynamics, 32(10), 1583–1600. https://doi.org/10.1080/07391102.2013.829756
  37. 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, 337, 15–23. https://doi.org/10.1016/j.jtbi.2013.07.016
  38. 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, 18(1), 229–237. https://doi.org/10.1007/s00894-011-1033-4
  39. Roterman, I., Konieczny, L., Jurkowski, W., Prymula, K., & Banach, M. (2011). Two-intermediate model to characterize the structure of fast-folding proteins. Journal of Theoretical Biology, 283(1), 60–70. https://doi.org/10.1016/j.jtbi.2011.05.027
  40. Roterman, I., Konieczny, L., Banach, M., & Jurkowski, W. (2011). Intermediates in the Protein Folding Process: A Computational Model. International Journal of Molecular Sciences, 12(8), 4850–4860. https://doi.org/10.3390/ijms11084850
  41. Banach, M., Stąpor, K., & Roterman, I. (2009). Chaperonin Structure—The Large Multi-Subunit Protein Complex. International Journal of Molecular Sciences, 10(3), 844–861. https://doi.org/10.3390/ijms10030844

Rozdziały w monografiach

  1. Banach, M., Konieczny, L., & Roterman, I. (2020). Proteins structured as spherical micelles. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 55–68. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00005-1
  2. Banach, M., Konieczny, L., & Roterman, I. (2020). Local discordance. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, p. 69. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00006-3
  3. Banach, M., Konieczny, L., & Roterman, I. (2020). The active site in a single-chain enzyme. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 71–78. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00007-5
  4. Banach, M., Konieczny, L., & Roterman, I. (2020). Protein-protein interaction encoded as an exposure of hydrophobic residues on the surface. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 79–89. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00008-7
  5. Banach, M., Konieczny, L., & Roterman, I. (2020). Ligand binding cavity encoded as a local hydrophobicity deficiency. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 91–93. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00009-9
  6. Banach, M., & Roterman, I. (2020). Solenoid – An amyloid under control. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 95–115. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00010-5
  7. Banach, M., Konieczny, L., & Roterman, I. (2020). Composite structures. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 117–133. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00011-7
  8. Banach, M., & Roterman, I. (2020). Non-amyloid structure of the Aβ(1–42) polypeptide in presence of a permanent chaperone. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 135–136. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00012-9
  9. Banach, M., & Roterman, I. (2020). Complexes Aβ(1–42) polypeptide with non-protein molecules. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 137–156. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00013-0
  10. Banach, M., & Roterman, I. (2020). Structure of selected fragments of Aβ(1–42) in complex with other proteins. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 157–172. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00014-2
  11. Banach, M., & Roterman, I. (2020). Amyloids identification based on fuzzy oil drop model. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 173–175. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00015-4
  12. Banach, M., & Roterman, I. (2020). Amyloid as a ribbon-like micelle. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 177–191. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00016-6
  13. Dułak, D., Gadzała, M., Banach, M., & Roterman, I. (2020). Analysis of alternative conformations of the Aβ(1–40) amyloid protein. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 193–206. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00017-8
  14. Banach, M., & Roterman, I. (2020). Specificity of amino acid sequence and its role in secondary and supersecondary structure generation. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 207–214. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00018-X
  15. Banach, M., Konieczny, L., & Roterman, I. (2020). Anti-amyloid drug design. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 215–231. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00019-1
  16. Banach, M., Konieczny, L., & Roterman, I. (2020). The hypothetical amyloid transformation of transthyretin. In: Roterman, I. (ed.), From Globular Proteins to Amyloids, pp. 233–240. Elsevier: Amsterdam. https://doi.org/10.1016/B978-0-08-102981-7.00020-8
  17. Banach, M., Konieczny, L., & Roterman, I. (2019). Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores. In: Kister, A. (ed.), Protein Supersecondary Structures, Methods in Molecular Biology, vol. 1958, pp. 347–378. Springer: New York. https://doi.org/10.1007/978-1-4939-9161-7_19
  18. Banach, M., Konieczny, L., & Roterman, I. (2018). Fuzzy Oil Drop Model Application—From Globular Proteins to Amyloids. In: Liwo, A. (ed.), Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series on Bio- and Neurosystems, vol. 8, pp. 639–658. Springer: Cham. https://doi.org/10.1007/978-3-319-95843-9_19
  19. Banach, M., Kalinowska, B., Konieczny, L., & Roterman, I. (2017). Possible Mechanism of Amyloidogenesis of V Domains. In: Roterman, I., & Konieczny, L. (eds.), Self-Assembled Molecules – New Kind of Protein Ligands, pp. 77–100. Springer: Cham. https://doi.org/10.1007/978-3-319-65639-7_5
  20. 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. In: Donev, R. (ed.), Advances in Protein Chemistry and Structural Biology, vol. 94, pp. 315–346. Academic Press: Oxford (obecnie Elsevier). https://doi.org/10.1016/B978-0-12-800168-4.00008-1
  21. Roterman, I., Konieczny, L., Banach, M., Marchewka, D., Barbara Kalinowska, Baster, Z., Tomanek, M., & Piwowar, M. (2014). Simulation of the Protein Folding Process. In: Liwo, A. (ed.), Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, vol. 1, pp. 599–638. Springer: Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28554-7_18
  22. Banach, M., Konieczny, L., & Roterman, I. (2013). Can the Structure of the Hydrophobic Core Determine the Complexation Site? In: Roterman, I. (ed.), Identification of Ligand Binding Site and Protein-Protein Interaction Area, Focus on Structural Biology, vol. 8, pp. 41–54. Springer: Dordrecht. https://doi.org/10.1007/978-94-007-5285-6_3
  23. Alejster, P., Banach, M., Jurkowski, W., Marchewka, D., & Roterman, I. (2013). Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins. In: Roterman, I. (ed.), Identification of Ligand Binding Site and Protein-Protein Interaction Area, Focus on Structural Biology, vol. 8, pp. 55–86. Springer: Dordrecht. https://doi.org/10.1007/978-94-007-5285-6_4
  24. Marchewka, D., Jurkowski, W., Banach, M., & Roterman, I. (2013). Prediction of Protein-Protein Binding Interfaces. In: Roterman, I. (ed.), Identification of Ligand Binding Site and Protein-Protein Interaction Area, Focus on Structural Biology, vol. 8, pp. 105–133. Springer: Dordrecht. https://doi.org/10.1007/978-94-007-5285-6_6
  25. Banach, M., Konieczny, L., & Roterman, I. (2012). The late-stage intermediate. In: Roterman, I. (ed.), Protein Folding in Silico, Woodhead Publishing Series in Biomedicine, vol. 22, pp. 21–37. Woodhead Publishing: Cambridge (obecnie Elsevier). https://doi.org/10.1533/9781908818256.21
  26. Banach, M., Marchewka, D., Piwowar, M., & Roterman, I. (2012). The divergence entropy characterizing the internal force field in proteins. In: Roterman, I. (ed.), Protein Folding in Silico, Woodhead Publishing Series in Biomedicine, vol. 22, pp. 55–77. Woodhead Publishing: Cambridge (obecnie Elsevier). https://doi.org/10.1533/9781908818256.55
  27. Banach, M., Konieczny, L., & Roterman, I. (2012). Ligand-binding-site recognition. In: Roterman, I. (ed.), Protein Folding in Silico, Woodhead Publishing Series in Biomedicine, vol. 22, pp. 79–93. Woodhead Publishing: Cambridge (obecnie Elsevier). https://doi.org/10.1533/9781908818256.79
  28. Banach, M., Konieczny, L., & Roterman, I. (2012). Use of the “fuzzy oil drop” model to identify the complexation area in protein homodimers. In: Roterman, I. (ed.), Protein Folding in Silico, Woodhead Publishing Series in Biomedicine, vol. 22, pp. 95–122. Woodhead Publishing: Cambridge (obecnie Elsevier). https://doi.org/10.1533/9781908818256.95
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