Publications

Books

• Irena Roterman (editor):
  Structure-function relation in proteins.
  Publisher: Transworld Research Network T.C., Trivandrum, Kerala, India (2009),
  ISBN: 978-817895-409-7.
  
  • Stopa B, Spólnik P, Konieczny L, Piekarska B, Rybarska J, Jagusiak A, Król M, Roterman I:
    Chapter 3:  Self-assembled organic molecules as non-standard protein-ligands – Experimental and computational studies.
  • Roterman I, Konieczny L, Bryliński M:
    Chapter 4:  Late-stage folding intermediate in silico model.
  • Roterman I, Bryliński M, Konieczny L:
    Chapter 5:  Active site recognition in silico.
  • Roterman I, Konieczny L, Brylinski M:
    Chapter 6:  Folding process in the presence of specific ligand.
• Irena Roterman-Konieczna:
  Prescription for Statistics.
  Publisher: Jagiellonian University Press (2009),
  ISBN: 978-83-233-2741-7.
• Irena Roterman, Michał Bryliński, Leszek Konieczny, Wiktor Jurkowski:
  Chapter 5: Early-stage protein folding - In Silico model  [pdf]
  In: Recent Advances in Structural Biology.
  Editor: Alexandre G. de Brevern,
  Publisher: Research Signpost, Trivandrum, Kerala, India (2007),
  ISBN: 978-81-308-0208-4.
• Leszek Konieczny, Irena Roterman:
  Strategia działania organizmu żywego [The master plan of a living organism].
  Publisher: ZamKor, Kraków (2000),
  ISBN: 83-85434-80-1.
  

Journal articles

80. Stopa B, Piekarska B, Konieczny L, Krol M, Rybarska J, Jagusiak A, Spolnik P, Roterman I, Urbanowicz B, Piwowar P, Lewinski K. (2009) Formation of amyloid-like aggregates through the attachment of protein molecules to a Congo red scaffolding framework ordered under the influence of an electric field. Cent. Eur. J. Chem.
79. Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wiśniowski Z, Sałapa K, Matczyńska E, Roterman I (2009) In silico structural study of random amino acid sequence proteins not present in Nature Chemistry and Biodiversity 6 2311-2336
78. K. Prymula, I. Roterman (2009) Structural entropy to characterize small proteins (70 aa) and their interactions. Entropy 11(1): 62-84 | Doi
77. M. Banach, I. Roterman (2009) Recognition of protein-protein complexation based on hydrophobicity distribution. Bioinformation 4(2): 98-100
76. V. Zobnina, I. Roterman (2009) Application of the fuzzy-oil-drop model to membrane protein simulation Proteins 77(2): 378-94 | Doi | PubMed
75. K. Prymula, I. Roterman (2009) Functional characteristics of small proteins (70 amino acid residues) forming protein-nucleic acid complexes J Biomol Struct Dyn 26(6): 663-77 | PubMed
74. W. Jurkowski, G. Porebski, K. Obtułowicz, I. Roterman (2009) Serum albumin complexation of acetylsalicylic acid metabolites Curr Drug Metab 10(5): 448-58 | PubMed
73. M. Banach, K. Stapor, I. Roterman (2009) Chaperonin structure - the large multi-subunit protein complex Int J Mol Sci 10(3): 844-61 | Doi | PubMed
72. G. Minervini, G. Evangelista, F. Polticelli, M. Piwowar, M. Kochanczyk, L. Flis, M. Malawski, T. Szepieniec, Z. Wiśniowski, E. Matczyńska, K. Prymula, I. Roterman (2008) Never born proteins as a test case for ab initio protein structures prediction Bioinformation 3(4): 177-9 | PubMed
71. M. Brylinski, L. Konieczny, A. Kononowicz, I. Roterman (2008) Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family. J Theor Biol 251(2): 275-285 | Doi | PubMed
70. M. Brylinski, M. Kochanczyk, E. Broniatowska, I. Roterman (2007) Localization of ligand binding site in proteins identified in silico. J Mol Model 13(6-7): 665-675 | Doi | PubMed
69. M. Brylinski, L. Konieczny, I. Roterman (2007) Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinform Res Appl 3(2): 234-260 | PubMed
68. M. Brylinski, K. Prymula, W. Jurkowski, M. Kochanczyk, E. Stawowczyk, L. Konieczny, I. Roterman (2007) Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol 3(5): e94 | Doi | PubMed
67. P. Spolnik, B. Stopa, B. Piekarska, A. Jagusiak, L. Konieczny, J. Rybarska, M. Krol, I. Roterman, B. Urbanowicz, J. Zieba-Palus (2007) The use of rigid, fibrillar Congo red nanostructures for scaffolding protein assemblies and inducing the formation of amyloid-like arrangement of molecules. Chem Biol Drug Des 70(6): 491-501 | Doi | PubMed
66. M. Brylinski, L. Konieczny, I. Roterman (2006) Ligation site in proteins recognized in silico. Bioinformation 1(4): 127-129 | PubMed
65. L. Konieczny, M. Brylinski, I. Roterman (2006) Gauss-function-Based model of hydrophobicity density in proteins. In Silico Biol 6(1-2): 15-22 | PubMed
64. M. Krol, I. Roterman, A. Drozd, L. Konieczny, B. Piekarska, J. Rybarska, P. Spolnik, B. Stopa (2006) The increased flexibility of CDR loops generated in antibodies by Congo red complexation favors antigen binding. J Biomol Struct Dyn 23(4): 407-416 | PubMed
63. M. Piwowar, J. Meus, P. Piwowar, Z. Wisniowski, J. Stefaniak, I. Roterman (2006) Tandemly repeated trinucleotides - comparative analysis. Acta Biochim Pol 53(2): 279-287 | PubMed
62. B. Stopa, J. Rybarska, A. Drozd, L. Konieczny, M. Krol, M. Lisowski, B. Piekarska, I. Roterman, P. Spolnik, G. Zemanek (2006) Albumin binds self-assembling dyes as specific polymolecular ligands. Int J Biol Macromol 40(1): 1-8 | Doi | PubMed
61. M. Brylinski, M. Kochanczyk, L. Konieczny, I. Roterman (2006) Sequence-structure-function relation characterized in silico. In Silico Biol 6(6): 589-600 | PubMed
60. M. Brylinski, L. Konieczny, I. Roterman (2006) Fuzzy-oil-drop hydrophobic force field—a model to represent late-stage folding (in silico) of lysozyme. J Biomol Struct Dyn 23(5): 519-528 | PubMed
59. M. Brylinski, L. Konieczny, I. Roterman (2006) Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem 30(4): 255-267 | Doi | PubMed
58. J. Meus, M. Brylinski, M. Piwowar, P. Piwowar, Z. Wisniowski, J. Stefaniak, L. Konieczny, G. Surowka, I. Roterman (2006) A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. Med Sci Monit 12(6): BR208-14 | PubMed
57. M. Brylinski, L. Konieczny, I. Roterman (2006) Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie 88(9): 1229-1239 | Doi | PubMed
56. P. Spolnik, L. Konieczny, B. Piekarska, J. Rybarska, B. Stopa, G. Zemanek, A. Drozd, M. Krol, I. Roterman, T. Wolska-Smolen, A. Skotnicki (2006) The use of the Congo red-related dye DBACR to recognize the heavy chain-derived abnormality of myeloma immunoglobulins. Arch Immunol Ther Exp (Warsz) 54(3): 217-221 | Doi | PubMed
55. B. Piekarska, A. Drozd, L. Konieczny, M. Krol, W. Jurkowski, I. Roterman, P. Spolnik, B. Stopa, J. Rybarska (2006) The indirect generation of long-distance structural changes in antibodies upon their binding to antigen. Chem Biol Drug Des 68(5): 276-283 | Doi | PubMed
54. M. Brylinski, L. Konieczny, P. Czerwonko, W. Jurkowski, I. Roterman (2005) Early-stage folding in proteins (in silico) sequence-to-structure relation. J Biomed Biotechnol 2005(2): 65-79 | Doi | PubMed
53. M. Brylinski, L. Konieczny, I. Roterman (2005) SPI—structure predictability index for protein sequences. In Silico Biol 5(3): 227-237 | PubMed
52. P. Spólnik, L. Konieczny, B. Piekarska, J. Rybarska, B. Stopa, G. Zemanek, A. Drozd, M. Król, I. Roterman, A. Skotnicki (2005) Congo red-derived supramolecular dyes as probes for disclosure of the aggregation tendency of abnormal monoclonal immunoglobulins. Polish Journal of Environmental Studies 14(?): 776-781
51. M. Krol, I. Roterman, B. Piekarska, L. Konieczny, J. Rybarska, B. Stopa, P. Spolnik, E. Szneler (2005) An approach to understand the complexation of supramolecular dye Congo red with immunoglobulin L chain lambda. Biopolymers 77(3): 155-162 | Doi | PubMed
50. M. Krol, I. Roterman, B. Piekarska, L. Konieczny, J. Rybarska, B. Stopa, P. Spolnik (2005) Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction. Proteins 59(3): 545-554 | Doi | PubMed
49. W. Jurkowski, M. Brylinski, L. Konieczny, Z. Wiiniowski, I. Roterman (2004) Conformational subspace in simulation of early-stage protein folding. Proteins 55(1): 115-127 | Doi | PubMed
48. J. Rybarska, B. Piekarska, B. Stopa, P. Spolnik, G. Zemanek, L. Konieczny, I. Roterman (2004) In vivo accumulation of self-assembling dye Congo red in an area marked by specific immune complexes: possible relevance to chemotherapy. Folia Histochem Cytobiol 42(2): 101-110 | PubMed
47. P. Spolnik, L. Konieczny, B. Piekarska, J. Rybarska, B. Stopa, G. Zemanek, M. Krol, I. Roterman (2004) Instability of monoclonal myeloma protein may be identified as susceptibility to penetration and binding by newly synthesized Congo red derivatives. Biochimie 86(6): 397-401 | Doi | PubMed
46. B. Piekarska, L. Konieczny, J. Rybarska, B. Stopa, P. Spolnik, I. Roterman, M. Krol (2004) Intramolecular signaling in immunoglobulins — new evidence emerging from the use of supramolecular protein ligands. J Physiol Pharmacol 55(3): 487-501 | PubMed
45. M. Krol, T. Borowski, I. Roterman, B. Piekarska, B. Stopa, J. Rybarska, L. Konieczny (2004) Force-field parametrization and molecular dynamics simulations of Congo red. J Comput Aided Mol Des 18(1): 41-53 | PubMed
44. M. Brylinski, W. Jurkowski, L. Konieczny, I. Roterman (2004) Limited conformational space for early-stage protein folding simulation. Bioinformatics 20(2): 199-205 | PubMed
43. W. Jurkowski, M. Brylinski, L. Konieczny, I. Roterman (2004) Lysozyme folded in silico according to the limited conformational sub-space. J Biomol Struct Dyn 22(2): 149-158 | PubMed
42. B. Stopa, B. Piekarska, L. Konieczny, J. Rybarska, P. Spolnik, G. Zemanek, I. Roterman, M. Krol (2003) The structure and protein binding of amyloid-specific dye reagents. Acta Biochim Pol 50(4): 1213-1227 | Doi | PubMed
41. P. Spolnik, B. Piekarska, B. Stopa, L. Konieczny, G. Zemanek, J. Rybarska, M. Krol, M. Nowak, I. Roterman (2003) The structural abnormality of myeloma immunoglobulins tested by Congo red binding. Med Sci Monit 9(4): BR145-53 | PubMed
40. L. Konieczny, I. Roterman (2003) Nowotwory — struktura czy organizacja? [Cancer — structure or organization?] Menopauza -- Prokreacja -- Starzenie -- Nowotwory ?(2): 87-91
39. J. Leluk, L. Konieczny, I. Roterman (2003) Search for structural similarity in proteins. Bioinformatics 19(1): 117-124 | PubMed
38. G. Zemanek, J. Rybarska, B. Stopa, B. Piekarska, P. Spolnik, L. Konieczny, I. Roterman, A. Bugajski (2003) Protein distorsion-derived mechanism of signal discrimination in monocytes revealed using Congo red to stain activated cells. Folia Histochem Cytobiol 41(3): 113-124 | PubMed
37. M. Krol, I. Roterman, B. Piekarska, L. Konieczny, J. Rybarska, B. Stopa (2003) Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain lambda. Biopolymers 69(2): 189-200 | Doi | PubMed
36. G. Zemanek, L. Konieczny, B. Piekarska, J. Rybarska, B. Stopa, P. Spolnik, B. Urbanowicz, M. Nowak, M. Krol, I. Roterman (2002) Egg yolk platelet proteins from Xenopus laevis are amyloidogenic. Folia Histochem Cytobiol 40(3): 311-318 | PubMed
35. J. Rybarska, B. Piekarska, B. Stopa, G. Zemanek, L. Konieczny, M. Nowak, M. Krol, I. Roterman, A. Szymczakiewicz-Multanowska (2001) Evidence that supramolecular Congo red is the sole ligation form of this dye for L chain lambda derived amyloid proteins. Folia Histochem Cytobiol 39(4): 307-314 | PubMed
34. B. Piekarska, L. Konieczny, J. Rybarska, B. Stopa, G. Zemanek, E. Szneler, M. Krol, M. Nowak, I. Roterman (2001) Heat-induced formation of a specific binding site for self-assembled Congo Red in the V domain of immunoglobulin L chain lambda. Biopolymers 59(6): 446-456 | Doi | PubMed
33. L. Konieczny, B. Piekarska, I. Roterman, J. Rybarska, B. Stopa, G. Zemanek (2001) Przeciwciała i nośniki leków w terapii celowanej - postęp i ograniczenia. Biotechnologia 3(54): 29-36
32. I. Roterman, M. KrUl, M. Nowak, L. Konieczny, J. Rybarska, B. Stopa, B. Piekarska, G. Zemanek (2001) Why Congo red binding is specific for amyloid proteins - model studies and a computer analysis approach. Med Sci Monit 7(4): 771-784 | PubMed
31. M. Skowronek, L. Konieczny, B. Stopa, J. Rybarska, B. Piekarska, A. Gorecki, M. Krol (2000) The conformational characteristics of Congo red, Evans blue and Trypan blue. Comput Chem 24(3-4): 429-450 | PubMed
30. M. Skowronek, I. Roterman, L. Konieczny, B. Stopa, J. Rybarska, B. Piekarska (2000) Why do Congo Red, Evans Blue and Trypan Blue differ in their complexation properties? Journal of Computational Chemistry ?(21): 656-667
29. M. Skowronek, I. Roterman, L. Konieczny, B. Stopa, J. Rybarska, B. Piekarska, A. Górecki, M. Król (2000) The structure of Congo Red, Evans Blue and Trypan Blue as seen in calculation using different methods. Computers and Chemistry ?(24): 429-450
28. B. Piekarska, J. Rybarska, B. Stopa, G. Zemanek, M. Krol, I. Roterman, L. Konieczny (1999) Supramolecularity creates nonstandard protein ligands. Acta Biochim Pol 46(4): 841-851 | PubMed
27. M. Skowronek, B. Stopa, L. Konieczny, J. Rybarska, B. Piekarska, E. Szneler, G. Bakalarski, I. Roterman (1998) Self-assembly of Congo Red — a theoretical and experimental approach to identify its supramolecular organisation in water and salt solutions. Biopolymers ?(46): 267-281
26. B. Stopa, M. Gorny, L. Konieczny, B. Piekarska, J. Rybarska, M. Skowronek, I. Roterman (1998) Supramolecular ligands: monomer structure and protein ligation capability. Biochimie 80(12): 963-968 | PubMed
25. I. Roterman, J. Rybarska, L. Konieczny, M. Skowronek, B. Stopa, B. Piekarska (1998) Congo Red bound to alpha-1-proteinase inhibitor as a model of supra-molecular ligand and protein complex Computers and Chemistry ?(22): 61-70
24. B. Stopa, L. Konieczny, B. Piekarska, I. Roterman, J. Rybarska, M. Skowronek (1997) Effect of self association of bis-ANS and bis-azo dyes on protein binding. Biochimie 79(1): 23-26 | PubMed
23. L. Konieczny, B. Piekarska, J. Rybarska, M. Skowronek, B. Stopa, B. Tabor, W. Dabros, R. Pawlicki, I. Roterman (1997) The use of congo red as a lyotropic liquid crystal to carry stains in a model immunotargeting system—microscopic studies. Folia Histochem Cytobiol 35(4): 203-210 | PubMed
22. B. Piekarska, M. Skowronek, J. Rybarska, B. Stopa, I. Roterman, L. Konieczny (1996) Congo red-stabilized intermediates in the lambda light chain transition from native to molten state. Biochimie 78(3): 183-189 | PubMed
21. L. Konieczny, B. Piekarska, I. Roterman, J. Rybarska, M. Skowronek, B. Stopa (1996) Perspektywy wykorzystania supramolekularnych struktur ciekłokrystalicznych do stabilizacji funkcyjnej konformacji białek. Wiadomo{\'s}ci Chemiczne ?(50): 29-42
20. I. Roterman (1995) Modelling the optimal simulation path in the peptide chain folding—studies based on geometry of alanine heptapeptide. J Theor Biol 177(3): 283-288 | Doi | PubMed
19. I. Roterman, L. Konieczny (1995) Geometrical analysis of structural changes in immunoglobulin domains' transition from native to molten state. Comput Chem 19(3): 247-252 | PubMed
18. I. Roterman (1995) The geometrical analysis of peptide backbone structure and its local deformations. Biochimie 77(3): 204-216 | PubMed
17. J. Rybarska, L. Konieczny, B. Piekarska, B. Stopa, I. Roterman (1995) The detection of specific acute phase serum protein complexes and immune complexes by congo red binding. J Physiol Pharmacol 46(2): 221-231 | PubMed
16. L. Konieczny, B. Piekarska, J. Rybarska, B. Stopa, B. Krzykwa, J. Noworolski, R. Pawlicki, I. Roterman (1994) Bis azo dye liquid crystalline micelles as possible drug carriers in immunotargeting technique. J Physiol Pharmacol 45(3): 441-454 | PubMed
15. B. Piekarska, I. Roterman, J. Rybarska, L. Koniczny, J. Kaszuba (1994) The melting of native domain structure in effector activation of IgG studied by using congo red as a specific probe. J Physiol Pharmacol 45(1): 147-162 | PubMed
14. I. Roterman, L. Konieczny, B. Stopa, J. Rybarska, B. Piekarska (1994) Heat-induced structural changes in the Fab fragment of IgG recognized by molecular dynamics stimulation—implications for signal transduction in antibodies. Folia Biol (Krakow) 42(3-4): 115-128 | PubMed
13. J. Kaszuba, L. Konieczny, B. Piekarska, I. Rotterman, J. Rybarska (1993) Bis-azo dyes interference with effector activation of antibodies. J Physiol Pharmacol 44(3): 233-242 | PubMed
12. I. Roterman (1993) Możliwości i znaczenie techniki komputerowej w symulacji zjawisk i modelowaniu struktur biologicznych. Przegląd lekarski ?(50): 229-232
11. I. Roterman, K. No, B. Piekarska, J. Kaszuba, R. Pawlicki, J. Rybarska, L. Konieczny (1993) Bis azo dyes—studies on the mechanism of complex formation with IgG modulated by heating or antigen binding. J Physiol Pharmacol 44(3): 213-232 | PubMed
10. J. Rybarska, L. Konieczny, I. Roterman, B. Piekarska (1991) The effect of azo dyes on the formation of immune complexes. Arch Immunol Ther Exp (Warsz) 39(3): 317-327 | PubMed
9. I. Roterman, M. Lambert, K. Gibson, H. Scheraga (1989) A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. J Biomol Struct Dyn 7(3): 421-453 | PubMed
8. I. Roterman, K. Gibson, H. Scheraga (1989) A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (Asn-Ala-Asn-Pro)9. J Biomol Struct Dyn 7(3): 391-419 | PubMed
7. J. Rybarska, B. Piekarska, L. Konieczny, I. Roterman (1988) The formation of soluble heat IgG aggregates for immunological studies. Arch Immunol Ther Exp (Warsz) 36(5): 609-622 | PubMed
6. I. Roterman, L. Konieczny, K. Bobrzecka, J. Rybarska, B. Ochalska (1987) The structure of the hinge region in Fab-Fc recombinant immunoglobulins and its relation to the effector activity of these molecules. Arch Immunol Ther Exp (Warsz) 35(3): 257-266 | PubMed
5. A. Bobrowski, I. Roterman (1986) Resolution of the polarographic methods. Resolution of linear potential sweep voltamperometry. Chemia Analityczna ?(31): 167-183
4. A. Górniak, L. Brongel, W. Jarzynowski, I. Roterman (1982) Obrażenia wielomiejscowe niekomunikacyjne Polski Przegląd Chirurgiczny ?(54): 631-637
3. J. Jurka, Z. Kolosza, I. Roterman (1982) Globular proteins, GU wobbling, and the evolution of the genetic code. J Mol Evol 19(1): 20-27 | PubMed
2. A. Górniak, L. Brongel, A. Wyroba, I. Roterman (1981) Komunikacyjne obrażenia wielomiejscowe Polski Przegląd Chirurgiczny ?(53): 145-151
1. Z. Żak, I. Małkiewicz, G. Pytasz (1979) Riboflavin-apoprotein interaction studied by infrared and Raman spectroscopy Flavins abd Flavoproteins Physicichemical Properties (Proceedings of an International Meeting on Flavins and Flavoproteins) ?(?): 39-50

Popular publications

• I Roterman (1999):
  Skąd się biorą nowe leki na koniec XX wieku?
  [Where the New drugs are coming from?]
  Lek w Polsce 9: 15-19.
• I. Roterman:
  Skąd się biorą nowe leki na początku XXI wieku?
  [How the new drugs are created at the beginning of XXI century]
  Lekarz domowy 1/2001.
• I Roterman (2001):
  Skąd się biorą nowe leki na początku XXI wieku?
  [New drugs – how are they discovered?]
  Ad Vocem 48-49: 48-51.
• I Roterman (2001):
  Bioinformatyka - narzędzie współczesnego medyka
  [Bioinformatics – the tool for modern medical doctors]
  Alma Mater 29: 10-12
• I Roterman:
  Wirtualny pacjent
  Alma Mater 119, XI 2009, str. 51-52