Publications and conferences

From Bioinformatics Group

Contents

2011

Journal articles

  1. Banach, M.; Prymula, K.; Jurkowski, W.; Konieczny, L. & Roterman, I. (2011), 'Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants.', J Mol Model.
  2. Banach, M.; Prymula, K.; Konieczny, L. & Roterman, I. (2011), '"Fuzzy oil drop" model verified positively.', Bioinformation 5(9), 375--377.
    [PMID 21383903]
    [Full text]
  3. Jurkowski, W.; Kułaga, T. & Roterman, I. (2011), 'Geometric parameters defining the structure of proteins--relation to early-stage folding step.', J Biomol Struct Dyn 29(1), 79--104.
  4. Marchewka, D.; Banach, M. & Roterman, I. (2011), 'Internal force field in proteins seen by divergence entropy.', Bioinformation 6(8), 300--302.
  5. Prymula, K.; Jadczyk, T. & Roterman, I. (2011), 'Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction.', J Comput Aided Mol Des 25(2), 117--133.
    [PMID 21104192]
    [Full text]
  6. Roterman, I.; Konieczny, L.; Banach, M. & Jurkowski, W. (2011), 'Intermediates in the Protein Folding Process: A Computational Model.', Int J Mol Sci 12(8), 4850--4860.
    [PMID 21954329]
    [Full text]
  7. Roterman, I.; Konieczny, L.; Jurkowski, W.; Prymula, K. & Banach, M. (2011), 'Two-intermediate model to characterize the structure of fast-folding proteins.', J Theor Biol 283(1), 60--70.
    [PMID 21635900
    [Full text]
  8. Spólnik, P.; Król, M.; Stopa, B.; Konieczny, L.; Piekarska, B.; Rybarska, J.; Zemanek, G.; Jagusiak, A.; Piwowar, P.; Szoniec, G. & Roterman, I. (2011), 'Influence of the electric field on supramolecular structure and properties of amyloid-specific reagent Congo red.', Eur Biophys J 40(10), 1187--1196.
    [PMID 21947508]
    [Full text]

Conference proceedings

  1. Piwowar M, Swatowski M, Roterman-Konieczna I, Porembski K (2011) Exons as an units In the identification and visualisation protein regions. Humane Genome Meeting, Dubaj/ United Arab Emirates
  2. Swatowski M, Piwowar M, Czudek B, Roterman-Konieczna I (2011) Determination of gene,s expression strenght influence on function/process/komponent in comparison to other expressed genes. Humane Genome Meeting, Dubaj/ United Arab Emirates

2010

Journal articles

  1. Stangel-Wójcikiewicz, K.; Majka, M.; Basta, A.; Stec, M.; Pabian, W.; Piwowar, M. & Chancellor, M. B. (2010), 'Adult stem cells therapy for urine incontinence in women.', Ginekol Pol 81(5), 378--381.
  2. Prymula K, Sałapa K, Roterman I. (2010) “Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids. J Mol Model 6(7): 1269-82
    [PMID 20084418] [Full Text]
  3. Stopa B, Piekarska B, Konieczny L, Król M, Rybarska J, Jagusiak A, Spólnik P, Roterman I, Urbanowicz, B, Piwowar P, Lewiński, K. (2010) 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. Central European Journal of Chemistry 8(1): 41-50.
    [Full Text ]
  4. Chmielnicki W, Roterman-Konieczna I and Stąpor K. (2010) An improved protein fold recognition with suport Victor machines "Expert Systems: The Journal of Knowledge Engineering".DOl: 10.1111/j.1468-0394.2010.00572.x
    [Full text]
  5. Chmielnicki W, Roterman-Konieczna I and Stąpor K. (2010) An improved protein fold recognition with suport Victor machines "Expert Systems: The Journal of Knowledge Engineering". DOl: 10.1111/j.1468-0394.2010.00572.x
    [Full text]
  6. Prymula, K.; Jadczyk, T. & Roterman, I. (2011), 'Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction.', J Comput Aided Mol Des 25(2), 117--133.
    [Full text]

2009

Books

  1. Statistics by Prescription. Editor: Roterman I, Publisher: Jagiellonian Universiyu Press, 2009, ISBN 978-83-233-2741-7
  2. Structure-Function Relation in Proteins. Editor: I. Roterman, Publisher: Transworld Research Network, 2009, ISBN: 978-81-7895-409-7.
    [Chapters at publisher's website] :

Active site recognition in silico. Roterman I, Bryliński M, Konieczny L, Structure-Function Relation in Proteins, 2009; 59-78; Editor: Roterman I.

Folding process In the presence of specific ligand. Roterman I, Konieczny L and Bryliński M, Structure-Function Relation in Proteins, 2009; 59-78; Editor: Roterman I.

Late stage holding intermediate in silico model, Roterman I, Konieczny L. Structure-Function Relation in Proteins, 2009; 59-78; Editor: Roterman I.

Self assembled organic molecules as non-standard protein ligands – Experimental and computational studiem, Stopa B, Spólnik P, Konieczny L, Piekarska B, Rybarska J, Jagusiak J, Król M and Roterman I. Structure-Function Relation in Proteins, 2009; 59-78; Editor: Roterman I.


Chapters in Books

  1. Piwowar M. Analiza materiału genetycznego - kompletne sekwencje genomów. w: red. Tadeusiewicz R., Augustyniak P. (red.), Podstawy inżynierii biomedycznej, Tom 2, Wydawnictwo AGH, Kraków 2009,s.493-512, ISBN 978-83-7464-263-7
    [Information about the book ]

Journal articles

  1. Stopa B, Piekarska B, Konieczny L, Król M, Rybarska J, Jagusiak A, Spólnik P, Roterman I, Urbanowicz B, Piwowar P, Lewiński K. (2009) Formation of amyloid-like aggregates through the attachment of protein molecules to a Congo red scaffolding framework ordered dunder the influence o fan electric field. "Central European Journal of Chemistry" 8(1):41-50
    [Full text]
  2. Banach, M. & Roterman, I. (2009), 'Recognition of protein complexation based on hydrophobicity distribution.', Bioinformation 4(3), 98--100.
  3. Banach, M.; Stapor, K. & Roterman, I. (2009), 'Chaperonin structure - the large multi-subunit protein complex.', Int J Mol Sci 10(3), 844--861.
    [PMID 21954329]
    [Full text]
  4. Jurkowski, W.; Porebski, G.; Obtułowicz, K. & Roterman, I. (2009), 'Serum albumin complexation of acetylsalicylic acid metabolites.', Curr Drug Metab 10(5), 448--458.
  5. Prymula K, Piwowar M, Kochańczyk 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. Chem Biodivers 6(12): 2311-2336.
    [PMID 20020465]
    [Full text]
  6. Jurkowski W, Porębski G, Obtułowicz K, Roterman I. (2009) Serum albumin complexation of acetylsalicylic acid metabolites. Curr Drug Metab 10(5): 448-58.
    [PMID 19689242]
  7. Zobnina V, Roterman I. (2009) Application of the fuzzy-oil-drop model to membrane protein simulation. Proteins 77(2): 378-94.
    [PMID 19455711]
    [Full text]
  8. Banach M, Stąpor K, Roterman I. (2009) Chaperonin structure - the large multi-subunit protein complex. Int J Mol Sci 10(3): 844-61.
    [PMID 19399224]
    [Free Full Text]
  9. Prymula K, Roterman I. (2009) Functional characteristics of small proteins (70 amino Acid residues) forming protein-nucleic acid complexes. J Biomol Struct Dyn 26(6): 663-78.
    [PMID 19385696] [Full Text]
  10. Prymula K, Roterman I. (2009) Structural entropy to characterize small proteins (70 aa) and their interactions, Entropy 11(1): 62-84.
    [Free Full Text]
  11. Roterman I. (2009) The XV Century Patients (as Presented on Wit Stwosz Altar) Diagnozed. "Bio-Algorithms and Med-Systems" "5" "(9)":147-152
    [[1]]

Conference proceedings

  1. Konieczny L, Spólnik P, Roterman I. (2009) Detektory biologiczne. Materiały IX Sympozjum “Modelowanie I pomiary w medycynie” pod redakcją prof. dr hab. Inż. Janusza Gajdy. 10-14 maja Krynica/Polska s. 45-46.
  2. Piwowar M.Jadczyk T(2009), 'Genes and function/process/component association on the basis of micorarray data VIII European Sympodium of The Protein Society; Zurich/Switzerland'
    [Conference website]
  3. Piwowar M, Kułaga T (2009), 'Microarray data analysis – two approaches Konferencja Użytkowników Komputerów Dużej Mocy; Marzec 12-13; Zakopane/Polska'.
  4. Matczyńska E, Szepieniec T, Piwowar. M. Roterman. I. (2009), 'Gene structure elements of “never born proteinsVIII European Sympodium of The Protein Society; Zurich/Switzerland'.
    [Conference website]

2008

Books

  1. Piwowar M, Roterman I. Projekt sekwencjonowania Ludzkiego Genomu.w: red. Tadeusiewicz R., Augustyniak P. (red.), Inżynieria biomedyczna. Księga współczesnej wiedzy tajemnej w wersji przystępnej i przyjemnej. Publisher: Wydawnictwo AGH, Kraków 2008, CD.

Journal articles

  1. Piwowar M, Matczyńska E, Ochlawski P, Kosibowicz M, Kość D, Swatowski M, Więcek P, Szepieniec T. (2008) GenFoSS–java application for presentation of coding stretches of Neper Born Proteins. "Bio-Algorithms and Med.-Systems". "4","7":9-16.
    [[2]]
  2. Porębski G, Obtułowicz K, P. M. R.-K. I. (2008), 'Association Between the N-Acetylation Genetic Polymorphism and Aspiryn-Induced Urticartia.', Bio-Algorithms and Med-System 4(8), 19-23
    [[3]]
  3. Marchewka D, Roterman I. (2008) "Ligands Database". "Bio-Algorithms and Med-System" "4" "(8)": 15-18
    [[4]]
  4. Minervini G, Evangelista G, Polticelli F, Piwowar M, Kochańczyk M, Flis L, Malawski M, Szepieniec T, Wiśniowski Z, Matczyńska E, Prymula K, Roterman I. (2008) Never born proteins as a test case for ab initio protein structures prediction. Bioinformation 3(4): 177-9.
    [PMID 19238243] [Free Full Text]
  5. Brylinski M, Konieczny L, Kononowicz A, Roterman I. (2008) Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpine family. J Theor Biol 251(2): 275-285.
    [PMID 18177901] [Full Text]
  6. Sarapata K, Sanak M, (2008) Bioinformatic Environment for Analyzing Large Scale Genome Sequence."Bio-Algorithms and Med-System" "4" "(8)":25-31


[[5]]

Conference proceedings

2007

Books

  1. Roterman I, Brylinski M, Konieczny L, Jurkowski W. Early-stage protein folding - In Silico model. - A chapter in Recent Advances in Structural Biology (2007, Research Signpost). Editor: Alexandre G. de Brevern, ISBN: 978-81-308-0208-4.
    [Free Full Text]

Journal articles

  1. Brylinski M, Kochańczyk M, Broniatowska E, Roterman I. (2007) Localization of ligand binding site in proteins identified in silico. J Mol Model 13(6-7): 665-75.
    [PMID 17394030] [Full Text]
  2. Brylinski M, Prymula K, Jurkowski W, Kochanczyk M, Stawowczyk E, Konieczny L, Roterman I (2007) Prediction of Functional Sites Based on the Fuzzy Oil Drop Model. PLoS Comput Biol 3(5): e94
    [PMID 17530916] [Free Full Text]

Conference proceedings

  1. Roterman I, Flis L, Jurkowski W, Prymula K, Broniatowska E, Kochańczyk M. Protein folding simulation rather than protein structure prediction – application to Never born proteins (NBP) - I; Protein Society Conference [Stockholm/Uppsala, Sweden, May 12.-16., 2007]
  2. Jurkowski W, Flis L, Broniatowska E, Prymula K, Kochanczyk M, Roterman I. Protein folding intermediate - early stage (ES) – loop identification – Never born proteins (NBP) - II; Protein Society Conference [Stockholm/Uppsala, Sweden, May 12.-16., 2007]
  3. Flis L, Jurkowski W, Prymula K, Broniatowska E, Kochanczyk M, Roterman I. Dynamics of early-stage structural forms – Never born proteins (NBP) - III; Protein Society Conference [Stockholm/Uppsala, Sweden, May 12.-16., 2007]
  4. Prymula K, Kochanczyk M, Broniatowska E, Flis L, Jurkowski W, Roterman I. Late stage (LS) structural form directed by the hydrophobic interaction - Never born proteins (NBP) - IV; Protein Society Conference [Stockholm/Uppsala, Sweden, May 12.-16., 2007]
  5. Broniatowska E, Prymula K, Kochanczyk M, Jurkowski W, Flis L, Roterman I. Biological function recognition (BFR) - Never born proteins (NBP) - V; Protein Society Conference [Stockholm/Uppsala, Sweden, May 12.-16., 2007]
  6. Kochanczyk M, Broniatowska E, Prymula K, Flis L, Jurkowski W, Roterman I. Simulation of folding in presence of ligand - Never born proteins (NBP) - VI; Protein Society Conference [Stockholm/Uppsala, Sweden, May 12.-16., 2007]

2006

Journal articles

  1. Stopa B, Rybarska J, Drozd A, Konieczny L, Król M, Lisowski M, Piekarska B, Roterman I, Spólnik P, Zemanek G. (2006) Albumin binds self-assembling dyes as specific polymolecular ligands. International Journal of Biological Macromolecules 40: 1-8.
    [PMID 16769109]
  2. Piekarska B, Drozd A, Konieczny L, Król M, Jurkowski W, Roterman I, Spólnik P, Stopa B, Rybarska J. (2006) The Indirect Generation of Long-distance Structural Changes in Antibodies upon their Binding to Antigen. Chem Biol Drug Des 68: 276-283
    [PMID 17177888]
  3. Król M, Roterman I, Drozd A, Konieczny L, Piekarska B, Rybarska J, Spólnik P, Stopa B. (2006) The Increased Flexibility of CDR Loops Generated in Antibodies by Congo Red Complexation Favors Antigen Binding. J of Biomol Struct Dynam, Vol.23, Nr 4.
    [PMID 16363876] [Free Full Text]
  4. Brylinski M, Kochańczyk M, Konieczny L, Roterman I. (2006) Sequence-structure-function relation characterized in silico. In Silico Biology 6(6):589-600. (Bioinformation Systems e.V.).
    [PMID 17518766] [Free Full Text]
  5. Meus J, Brylinski M, Piwowar M, Piwowar P, Wisniowski Z, Stefaniak J, Konieczny L, Surowka G, Roterman I. (2006) A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. Med Sci Monit 12: 208-214.
    [PMID 6733478] [Free Full Text]
  6. Konieczny L, Brylinski M, Roterman I. (2006) Gauss-function-based model of hydrophobicity density in proteins. In Silico Biology 6: 15-22.
    [PMID 16789910] [Free Full Text]
  7. Brylinski M, Konieczny L, Roterman I. (2006) Fuzzy-oil-drop hydrophobic force field - a model to represent late-stage folding (in silico) of lysozyme. J Biomol Struct Dynam 23: 519-527.
    [PMID 16494501] [Free Full Text]
  8. Brylinski M, Konieczny L, Roterman I. (2006) Hydrophobic collapse in late-stage folding (in silico) of bosine pancreatic trypsin inhibitor. Biochimie 88: 1229-1239
    [PMID 16647798]
  9. Brylinski M, Konieczny L, Roterman I. (2006) Ligation site in proteins recognized in silico. Bioinformation 1: 127-129.
    [Free Full Text]
  10. Brylinski M, Konieczny L, Roterman I. (2006) Hydrophobic collapse in (in silico) protein folding. Comp Biol Chem 30: 255-267.
    [PMID 16798094]

Conference proceedings

  1. Broniatowska E, Stepien O, Roterman I. PLDB - Protein Ligands DataBase. Modeling & Design of Molecular Materials 2006; Program & Book of Abstracts [Wroclaw, Poland; September 10.-15., 2006].
  2. RotermanI. Computer Modeling in Drug Design. Cracow Computational Science Workshop. [Kraków, Poland; April 3.-4., 2006].
  3. Roterman I, Brylinski M. Co to jest bioinformatyka? VIII 'Sympozjum Modelowanie i Pomiary w Medycynie', [Krynica, Poland; May 14.-18., 2006].
  4. Roterman I, Brylinski M, Jurkowski W. Simulation of protein folding process. 3rd Central European Conference Chemistry Towards Biology; [Jagiellonian University, Faculty of Chemistry; Krakow, Poland; September 8.-12., 2006].
  5. Roterman I, Kochanczyk M, Malawski M, Piwowar M, Szepieniec T. The Quest for Pharmacology Active 'Never Born Proteins' within EUChinaGRID Project. Cracow Grid Workshop; [Krakow, Poland, October 15.-18., 2006].


2005

Journal articles

  1. Spólnik P, Konieczny L, Piekarska B, Rybarska J, Stopa B, Zemanek G, Drozd A, Król M, Roterman I, Wolska-Smoleń T, Skotnicki AB (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.
  2. Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B, Spólnik P, Szneler E. (2005) An approach to understand the complexation of supramolecular dye Congo red with immunoglobulin L chain lambda. Biopolymers 77: 155-162
    [PMID 15641119]
  3. Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B, Spólnik P. (2005) Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction. Proteins Struct Func Bioinform 59: 545-554
    [PMID 15778960]
  4. Brylinski M, Konieczny L, Roterman I. (2005) Structural motifs responsible for biological function are already present in proteins during early-stage folding (in silico) MISSING 5: 227-237.
  5. Brylinski M, Konieczny L, Czerwonko P, Jurkowski W, Roterman I. (2005) Early-stage folding in proteins (in silico) - sequence to structure relation. J Biomed Biotechnol 2: 65-79
    [PMID 16046811] [Free FullText].

Conference proceedings

  1. Jurkowski W, Szymaniak E. Analysis of stability of complexes of isonicotinic acid hydrazid derivatives with beta-cyclodekstrin. Joint Meeting of the Medicinal Chemistry [Vienna; June 2005].
  2. Jurkowski W, Roterman I. Protein active site in the early-stage folding structure. VIth European Meeting of The protein Society [Barcelona; May 2005].


2004

Journal articles

  1. Brylinski M, Konieczny L, Roterman I. (2004) SPI – Structure Predictability Index for protein sequences. In Silico Biology 4: 0022.
  2. Rybarska J, Piekarska B, Stopa B, Spólnik P, Zemanek G, Konieczny L, Roterman I. (2004) In vivo accumulation of self-assembling dye Congo red in an area marked by specific immune complexes: possible relevance to chemotherapy. Folia Histochemica et Cytobiologica, Vol. 42, No. 2: 101-110.
  3. Spólnik P, Konieczny L, Piekarska B, Rybarska J, Stopa B, Zemanek G, Król M, Roterman I (2004) Instability of monoclonal myeloma protein may be identified as susceptibility to penetration and binding by newly synthesized Congo red derivatives. Biochimie 86: 397-401.
  4. Piekarska B, Konieczny L, Rybarska J, Stopa B, Spólnik P, Roterman I, Król M. (2004) Intramolecular signaling in immunoglobulines – new evidence emerging from the use of supramolecular protein ligands. Journal of Physiology and Pharmacology 55, 3:487-501.
  5. Jurkowski W, Brylinski M, Konieczny L, Roterman I. (2004) Lysozyme folded in silico according to the limited conformational sub-space. J of Biomol Struct Dynam 22, 2:149-157.
  6. Brylinski M, Jurkowski W, Konieczny L, Roterman I. (2004) Limitation of conformational space for proteins – early-stage folding simulation of human α and β hemoglobin chains. TASK-Quarterly 8:1001-1010.
  7. Król M, Borowski T, Roterman I, Piekarska B, Stopa B, Rybarska J, KoniecznyL. (2004) Force-field parametrization and molecular dynamics of Congo red. Journal of computer aided molecular design 18, 1:41-53.
  8. Jurkowski W, Brylinski M, Konieczny L, Wisniowski Z, Roterman I. (2004) The conformational sub-space in simulation of early-stage protein folding Proteins: Structure, Function and Bioinformatics 55, 115-127.
  9. Nowak M. (2004) Immunoglobulin kappa light chain and its amyloidogenic mutants: a molecular dynamics study. Proteins: Structure, Function and Bioinformatics 55, 11-21.
  10. Brylinski M, Jurkowski W, Konieczny L, Roterman I. (2004) Limited conformational space for early-stage protein folding simulation. Bioinformatics 20, 2:199-205.

Conference proceedings

  1. Meus J, Stefaniak J. Analiza i klasyfikacja danych w aspekcie współczynnika Z. SKAD, [Białowieża, Poland; September 15-17.09.2004].
  2. Meus J, Stefaniak J .Asymmetrical measures of Association in contingency tables. Krajowa Konferencja Zastosowań Matematyki w Biologi I Medycynie [Święty Krzyż, Poland; 22-25.09.2004].
  3. Piwowar M, Meus J, Roterman I. Analiza zawartości mikrosatelitów (CAG)n w genomach wybranych organizmów oraz w mRNA ludzkim. Sztuczna Inteligencja w inżynierii biomedycznej [AGH, Kraków, Poland; 19.10.2004].


2003

Journal articles

  1. Król M. (2003) Analysis of the effect of electrostatic energy truncation in molecular dynamics simulations of Immunoglobulin G Light Chain Dimer. Journal of Molecular Modeling 9, 5:316-324.
  2. Spólnik P, Piekarska B, Stopa B, Konieczny L, Zemanek G, Rybarska J, Król M, Nowak M, Roterman I. (2003) The structural abnormality of myeloma immunoglobulins tested by Congo red binding. Medical Science Monitor 9, 4:185-193.
  3. Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B (2003) Local and long-range structural effects caused by the removal of the N-terminal polypaptide fragment from immunoglobulin L chain lambda. Biopolymers 69, 2:189-200.
  4. Król M (2003) Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. Journal of Computational Chemistry 24, 5:531-546.
  5. Leluk J, Konieczny L, Roterman I (2003) Search for similarity in proteins. Bioinformatics 19, 1:117-124.

Conference proceedings

  1. Zobnina W, Kieć-Kononowicz K, Handzlik J, Roterman I, Nowak M. Synthesis and conformational analysis of some pyrimido[2,1-f]purindiones as an attempt at searching for new A2A adenosine receptor antagonists. Polish-Austrian-German-Hungarian-Italian Joint Meeting on Medicinal Chemistry, [Kraków, Poland; 15-18.10.2003].
  2. Król M, Roterman I, Piekarska B, Stopa B, Rybarska J, Konieczny L. Functionally induced structural changes in immunoglobulin G domains registered by liquid crystal binding – a computer simulation." ECCB European Conference on Computational Biology [Paris; September 2003].
  3. Nowak M, Roterman I, Konieczny L, Piekarska B, Rybarska J, Stopa B. Bpti transformed to amyloid form in vitro and in silico. 5th European Symposium of the Protein Society [Florence, Italy; 29.03-2.04.2003].
  4. Jurkowski W, Bryliński M, Wisniowski Z, Konieczny L, Roterman I. Structural information coded in the Amino Acid Sequence. 5th European Symposium of The Protein Society [Florence; 29.03-2.04.2003]. Protein Science '12, Suppl.1, p.163.
  5. Brylinski M, Jurkowski W, Roterman I. Limitation of Conformational Space for Early Stages of Protein Holding Simulation. 5th European Symposium of The Protein Society [Florence; 29.03-2.04.2003]. Protein Science 12, Suppl.1, p.164.
  6. Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B. Role of the N-terminal fragment of immunoglobulin chain lambda in the stability of the protein (domain). Theoretical studies on protein - congo Red complexes. 5th European Symposium of The Protein Society [Florence; 29.03-2.04.2003]. Protein Science 12, Suppl.1, p.186.
  7. Piwowar M, Meus J, Wiśniowski Z, Roterman I, Grzybowski P. Characteristics of simple repeats sequences in humane genome. 5th European Symposium of the Protein Society [Florence; 29.03-2.04.2003]. Protein Science 12, Suppl.1, p. 106.
  8. Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B. Role of the N-terminal fragment of immunoglobulin chain lambda in the stability of the protein (domain). Theoretical studies on protein – congo Red complexes. 5th European Symposium of The Protein Society [Florence; 29.03-2.04.2003]. Protein Science 12, Suppl.1, p.186.


2002 and before

Journal articles

  1. G. Zemanek, L. Konieczny, B. Piekarska, J. Rybarska, B. Stopa, P. Spólnik, B. Urbanowicz, M. Nowak, M. Król, I. Roterman "Egg yolk platelet proteins from Xenopus laevis are amyloidogenic." Folia Histochemica et Cytobiologica 40(3), 311-318 (2002)
  2. B. Piekarska, L. Konieczny, J. Rybarska, B. Stopa, G. Zemanek, E. Szneler, M. Król, M. Nowak, I. Roterman "The heat induced formation of a specific binding site for self-assembled Congo red in V domain of immunoglobulin chain l." Biopolymers 59(6), 446-456 (2001)
  3. J. Rybarska, B. Piekarska, B. Stopa, G. Zemanek, L. Konieczny, M. Nowak, M. Król, I. Roterman, A. Szymczakiewicz-Multanowska "Evidence that supramolecular Congo red is the sole ligation form of this dye for L chain l derived amyloid proteins." Folia Histochemica et Cytobiologica 39, 307-314 (2001)
  4. L. Konieczny, B. Piekarska, I. Roterman, J. Rybarska, B. Stopa, G.Zemanek "Przeciwciała i nośniki leków w terapii celowanej - postęp i ograniczenia." Biotechnologia 3(54), 29-36 (2001)
  5. I. Roterman, M. Król, M. Nowak, L. Konieczny, J. Rybarska, B. Stopa, B. Piekarska, G. Zemanek "Why Congo red binding is specific for amyloid proteins?" Medical Science Monitor 7(4), 771-784 (2001)
  6. M. Skowronek, I. Roterman, L. Konieczny, B. Stopa, J. Rybarska, B. Piekarska "Why do Congo Red, Evans Blue and Trypan Blue differ in their complexation properties? Journal of Computational Chemistry 21(8), 656-667 (2000)
  7. M. Skowronek, I. Roterman, L. Konieczny, B. Stopa, J. Rybarska, B. Piekarska, A. Górecki, M. Król "The conformational characteristics of Congo red, Evans blue and Trypan blue." Computers and Chemistry 24(3-4), 429-450 (2000)
  8. B. Piekarska, J. Rybarska, B. Stopa, G. Zemanek, M. Król, I. Roterman, L. Konieczny "Supramolecularity creates nonstandard ligands." Acta Biochimica Polonica 46(4), 841-851 (1999)
  9. B.Stopa, M.Górny, L.Konieczny, B. Piekarska, J.Rybarska, M.Skowronek, I.Roterman "Supramolecular ligands: Monomer structure and protein ligation capability." Biochimie80, 963-968 (1998)
  10. M.Skowronek, B.Stopa, L.Konieczny, J.Rybarska, B.Piekarska, E.Szneler, G.Bakalarski, I.Roterman "Self-Assembly of Congo Red - A theoretical and experimental approach to identify its supramolecular organization in water and salt solutions." Biopolymers 46, 267-281 (1998)
  11. Marek Skowronek "Supramolekularna organizacja Czerwieni Kongo, warunkująca specyficzne dla funkcji oddziaływanie z białkiem. Praca doktorska 1998.
  12. I.Roterman, J.Rybarska, L.Konieczny, M.Skowronek, B.Stopa, B.Piekarska, G.Bakalarski "Congo Red bound to a-1-proteinase inhibitor as a model of supramolecular ligand and protein complex." Computers and Chemistry 22(1), 61-70 (1998)
  13. L.Konieczny, B.Piekarska, J.Rybarska, M.Skowronek, B.Stopa, B.Tabor, W. Dąbroś, R.Pawlicki, I.Roterman "The use of Congo Red as a lyotropic liquid crystal to carry stains in a model immunotargeting system - microscopic studies". Folia Histochemica et Cytobiologica 35, 203-210 (1997)
  14. B.Stopa, L.Konieczny, B.Piekarska, I.Roterman, J.Rybarska, M.Skowronek "Effect of self association of bis-ANS and bis-azo dyes on protein binding." Biochimie 79(1), 23-26 (1997)
  15. B. Piekarska, M. Skowronek, J. Rybarska, B. Stopa, I. Roterman, L. Konieczny "Congo Red - stabilized intermediates in the lambda light chain transition from native to molten state." Biochimie 78(3), 183-189 (1996)
  16. L. Konieczny, B. Piekarska, I. Roterman, J. Rybarska, M. Skowronek, B. Stopa "Perspektywy wykorzystania supramolekularnych struktur ciekłokrystalicznych do stabilizacji funkcyjnej konformacji białek" Wiadomości Chemiczne 50, 29-42 (1996)
  17. J. Rybarska, L. Konieczny, B. Piekarska, B. Stopa, I. Roterman "The detection of specific acute phase serum protein complexes and immune complexes by Congo Red binding to serum proteins components." J. Physiol. Pharmacol.46,221-231 (1995)
  18. I. Roterman "Modelling the optimal simulation path in the peptide chain folding - Studies based on geometry of alanine heptapeptide." J. Theoretical Biology 177(3), 283-288 (1995)

Conference proceedings

  1. Piwowar Monika, Grzybowski Piotr, Meus Jan, Wiśniowaski Zdzisław, Roterman Irena, „Characteristics of simple-repeats in Humane Genome”, Gliwickie Spotkania Naukowe, 2002, Gliwice, Poland
  2. M Krol, M. Nowak, I. Roterman, B. Piekarska, J. Rybarska, B. Stopa, G. Zemanek, L. Konieczny "Interaction of immunoglobulin light chain dimer with Congo red - dynamics study." IUPAB, 2002, Buenos Aires, Argentina
  3. Piekarska B, Konieczny L, Rybarska J, Stopa B, Zemanek G, Roterman I, Król M, Nowak M. "Znaczenie N-końcowego rejonu cząsteczki dla stabilności i elastyczności łańcucha lekkiego lambda immunoglobuliny. N-terminal fragment of light chain lambda of IgG influence on the stability and elasticity of immunoglobulin." XXXVIII Zjazd Polskiego Towarzystwa Biochemicznego Wrocław 2002 Abstract str 40 (I-P-35)
  4. Zemanek G, Konieczny L, Piekarska B, Rybarska J, Stopa B, Roterman I, Król M, Nowak M. "Amyloidogenne własności białek z płytek żółtkowych afrykańskiej żaby szponiastej (Xenopus laevis). Amyloidogeneity of yolk platelets in Xenopus leavis." XXXVIII Zjazd Polskiego Towarzystwa Biochemicznego Wrocław 2002 Abstract str 418 (XIII-P-16)
  5. Spólnik P, Piekarska B, Stopa B, Konieczny L, Zemanek G, Rybarska J, Król M, Nowak M, Roterman I. "Strukturalne anomalie monoklonalnych immunoglobulin wykrywane wiązaniem czerwieni Kongo." "Structural abnormality of monoclonal immunoglobulins detected by Congo red binding." XXXVIII Zjazd Polskiego Towarzystwa Biochemicznego Wrocław 2002 Abstract str 425 (XIII-P-28)
  6. M.Król, M. Nowak, I Roterman, B. Stopa, B. Piekarska, J. Rybarska, L. Konieczny "Interaction of immunoglobulin light chain dimer with Congo red - dynamics study." 4th European Symposium of The Protein Society, Paris 2001, Protein Science, Vol10, Suppl.1, April 2001, pp.95
  7. M. Nowak, M. Król, I. Roterman, L. Konieczny, J. Rybarska, B. Stopa, B. Piekarska, G. Zemanek "The effect of point mutations on amyloidogenicity of monoclonal Ig light chain dimer." 4th European Symposium of The Protein Society Paris2001 Protein Science, Vol10, Suppl.1, April 2001, pp.95
  8. I.Roterman, M.Nowak, M. Król, L. Konieczny, J. Rybarska, B. Stopa, B. Piekarska, G. Zemanek "Limitations in molecular dynamics simulations." The 1st Workshop on Parallel Computing in Biomolecular Simulations 1-3 September 2001, The Technical University of Gdansk, Poland
  9. T. Borowski, M. Król, M. Chruszcz, E. Brocaawik "First Pronciple calculations for the non-heme iron centers of lipoxygenases." The 1st Workshop on Parallel Computing in Biomolecular Simulations 1-3 September 2001, The Technical University of Gdansk, Poland
  10. M.Nowak, M. Król, I.Roterman L. Konieczny, J. Rybarska, B. Stopa, B. Piekarska, G. Zemanek "Is the molecular dynamics simulation able to predict the amyloid formation?" The 1st Workshop on Parallel Computing in Biomolecular Simulations 1-3 September 2001, The Technical University of Gdansk, Poland
  11. T. Borowski, M. Król, M. Chruszcz, E. Brocaawik "First Pronciple calculations for the non-heme iron centers of lipoxygenases." Austrian-Czech-Polish-Slovak Symposium on Qunatum Chemistry, September 27-30 2001, Ustro--Jaszowiec, Poland
  12. T. Borowski, M. Król, Maksymilian Chruszcz, Ewa Brocławik "First Principle calculations for the non-heme iron centers of lipoxygenases." 20th European Crystalographic Meeting ECM20 Kraków 2001, Crystallography in Natural Sciences and Technology August 25th-31st, 2001
  13. T. Borowski, M. Król, M. Chruszcz, E. Brocławik "First Principle calculations for the non-heme iron centers of lipoxygenases." Model(l)ing 2001, Erlangen, September 16-21, 2001
  14. M. Król, T. Borowski, M. Nowak, I. Roterman 'Molecular modelling of Congo red.' Model(l)ing 2001, Erlangen, September 16-21, 2001
  15. M. Król, M. Nowak, I. Roterman "Comparison of various implicit solvation methods im molecular dynamics simulations of IgG light chain dimer." International Conference on Conformation of Peptides, Proteins and Nucleic Acids, Debrzyno 2000
  16. M. Nowak, M. Król, I. Roterman "Molecular dynamics study of immunoglobulin light chain dimer." International Conference on Conformation of Peptides, Proteins and Nucleic Acids, Debrzyno 2000
  17. M. Król, M. Nowak, I. Roterman "Computer Simulations in Molecular Modelling." SGI Users' Conference, Kraków 2000
  18. B. Piekarska, L. Konieczny, I. Roterman, M. Król, J. Rybarska, B. Stopa "Kompleks łańcucha lekkiego (lambda) immunoglobuliny z supramolekularnym ligandem - czerwieni Kongo." XXXVI Zjazd Polskiego Towarzystwa Biochemicznego, Pozna 2000
  19. L. Konieczny, J. Rybarska, B. Stopa, B. Piekarska, G. Zemanek, M. Król, M. Nowak, I. Roterman "Układy ciekłokrystaliczne jako potencjalne nośniki leków w technice immunotargetingu." XXXVI Zjazd Polskiego Towarzystwa Biochemicznego, Poznań 2000
  20. I. Roterman, L. Konieczny, M. Król, M. Nowak, J. Rybarska, B. Piekarska, B. Stopa, G. Zemanek "Monomeryczna i supramolekularna forma czerwieni Kongo w kompleksach z białkami." XXXVI Zjazd Polskiego Towarzystwa Biochemicznego, Pozna 2000
  21. I. Roterman, M. Król, M. Nowak, L. Konieczny, J. Rybarska, B. Piekarska, B. Stopa, G. Zemanek "Układ ciekołokrystaliczny ligandu w kompleksie z białkiem" Krajowe sympozjum "Symulacje MD w Polsce" Gdassk 2000
  22. I.Roterman, L.Konieczny, J.Rybarska, B.Piekarska, B.Stopa "Congo Red Bound to b-structural polypeptide chains." 13-th Symposium of The Protein Society, Boston, USA 24-28 July 1999.
  23. M. Król, I. Roterman, L. Konieczny, J. Rybarska, B. Piekarska, B. Stopa, M. Górny 'Distribution of electrostatic potential around molecules forming supramolecualr structures.' VIII Ogólnopolskie Sympozjum, Konformacja peptydów, białek i kwasów nukleinowych, Rynia, 1999
  24. M.Skowronek, I.Roterman, L.Konieczny, B.Stopa,J. Rybarska, B.Piekarska, A.Górecki, M.Król "Structure of Congo Red, Evans Blue and Trypan Blue as seen in calculation using different methods." 5-th Conference Computers in Chemistry'99, Szklarska Poręba, July 1-6 1999.
  25. I.Roterman, M.Skowronek, L.Konieczny, B.Stopa, J.Rybarska, B.Piekarska, M.Górny "Liquid crystals as supramolecular ligands." High Performance Computing on Hewlett-Packard Systems (Annual Conference of the HP2EUG), Zurich, Switzerland, 14-16 October 1998
  26. I.Roterman, M.Skowronek, L.Konieczny, J.Rybarska, B.Stopa, B.Piekarska "Computer aided drug design." High Performance Computing on Hewlett-Packard Systems, Kraków, 5-8 November 1997.
  27. I.Roterman, J.Rybarska, L.Konieczny, M.Skowronek, B.Stopa, B.Piekarska, G.Bakalarski "Congo Red bound to a-1-proteinase inhibitor as a model of supramolecular ligand and protein complex." 11-th Symposium of The Protein Society, Boston, USA, 12-16 July 1997
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