Department of Bioinformatics and Telemedicine

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.

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

Contact form

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)

Links

Interests

bioinformatics, computational geometry, computer science, data analysis, data visualization, hydrophobic core, optimization algorithms, protein folding, protein-protein interaction, python programming, web services and databases

Conducted courses

  • Telemedycyna z elementami symulacji medycznej
  • Informatyka i Statystyka Medyczna 2/2
  • Telemedicine with Elements of Medical Simulation
  • Computer science and medical statistics 1/2
  • Computer science and medical statistics 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

Activity in the scientific community

Research articles

  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

Chapters in collections

  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 (currently 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 (currently 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 (currently 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 (currently 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 (currently Elsevier). https://doi.org/10.1533/9781908818256.95
 
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