Uniwersytet Jagielloński Collegium Medicum Zakład bioinformatyki i telemedycyny

Prof. dr hab. Irena Roterman-Konieczna

Bibliografia

 

 

2012

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. J Mol Model. 18(1):229-37.

Spólnik P, Konieczny L, Roterman I, Markiewicz M (2012) Biological clock - is the need for a clock a common issue for cells and computers? Bio-Algorithms and Med-Systems 8(2),2012, 185-193.

Sałapa K, Kalinowska B, Jadczyk T, Roterman I. (2012) Measurement of hydrophobicity distribution in proteins – complete redundant protein data bank Bio-Algorithms and Med-Systems 8(2), 195-206.

Sałapa K, Kalinowska B, Jadczyk T, Roterman I. (2012) Measurement of hydrophobicity distribution in proteins –Non-redundant Protein Data Bank Bio-Algorithms and Med-Systems 8(3), 327-337.

Konieczny L, Markiewicz M, Piwowar P, Roterman I. (2012) Technical solutions for bio-measurements Bio-Algorithms and Med-Systems 8(4), 339-349.

Marchewka D, Roterman I, Strus M, Śpiewak K, Majka G. (2012) Structural analysis of the lactoferrin iron binding pockets Bio-Algorithms and Med-Systems 8(4), 351-359.

Ciepiela E, Jadczyk, Harężlak D, Kasztelnik M, Nowakowski P, Dyk G, Malawski M, Bubak M, Roterman I. (2012) Computations of protein hydrophobicity profile as virtual experiment in gridspace virtual laboratory Bio-Algorithms and Med-Systems 8(4), 361-372.

2011

Spólnik P, Król M, Stopa B, Konieczny L, Piekarska B, Rybarska J, Zemanek G, Jagusiak A, Piwowar P, Szaniec G, Roterman I. Influence of the electric field on supramolecular structure and properties of amyloid-specific reagent, Congo red, Eur Biophys J. 2011 October; 40(10): 1187–1196.

Banach M, Prymula K, Jurkowski W, Konieczny L, Roterman I. Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants. J Mol Model. 2012 January; 18(1): 229–237. Published online 2011 April 27. doi:  10.1007/s00894-011-1033-4

Evangelista G, Minervini G, Polticelli F, Malawski M, Szepieniec T, Flis L, Prymula K, Kochanczyk M, Matczynska E, Wisniowski Z, Salapa K, Banach M, Roterman I. Ab initio Protein structure prediction – the hydrophobicity distribution analysis. Bio-Algorithms and Med-Systems 2011, 7, 5-12.

Marchewka D, Banach M, Roterman I. Internal force field in proteins seen by divergence entropy. Bioinformation. 2011;6(8):300-2.

Jurkowski W, Kulaga T, Roterman I. Geometric parameters defining the structure of proteins- -relation to early-stage folding step. J Biomol Struct Dyn. 2011 29(1):79-104.

Roterman I, Konieczny L, Jurkowski W, Prymula K, Banach M. Two-intermediate model to characterize the structure of fast-folding proteins. J Theor Biol. 2011 283(1):60-70.

Banach M, Prymula K, Konieczny L, Roterman I. Fuzzy oil drop" model verified positively. Bioinformation. 2011;5(9):375-7.

Prymula K, Jadczyk T, Roterman I. Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. J Comput Aided Mol Des. 2011, 25(2):117-33.

Roterman I, Konieczny L, Banach M, Jurkowski W. Intermediates in the Protein Folding Process: A Computational Model. Int. J. Mol. Sci. 2011, 12(8), 4850-4860

Marchewka D, Roterman I. Internal force field in proteins. Think Mind 2011, May 22, 2011 to May 27, 2011 Venice 110-115.

 

2010

Prymula K, Sałapa K, Roterman I. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids. J Mol Model. 2010 Jul;16(7):1269-82. Epub 2010 Jan 19.

Stopa B, Piekarska B, Konieczny L, Król M, Rybarska J, Jagusiak A, Spólnik P, Roterman I, Urbanowicz, B, Piwowar P, Lewiński, K. 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, 2010

 

2009

Banach M, Prymula K, Konieczny L, Roterman I. Fuzzy oil drop model verified positively, Bioinformation 2011, 5, 375-377

Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wisniowski Z, Salapa K, Matczynska E, Roterman I.,  In silico structural study of random amino acid sequence proteins not present in Nature, Chemistry and Biodiversity 6, 2311-2336, 2009

Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I., Prediction of functional sites based on the fuzzy oil drop model.  PLoS-Computational Biology 2009

Prymula K, Roterman I., Structural entropy to characterize small proteins (70 aa) and their interactions. Entropy, 11, 62-84, 2009

Banach M, Stąpor K, Roterman I., Chaperonin structure – the large multi-subunit protein complex. Int. J. Mol. Sci. 10, 844-861, 2009

Jurkowski W, Porębski G, Obtułowicz K, Roterman I. Serum albumin complexation of acetylsalicylic acid metabolites. Curr Drug Metab 2009, 10(5):448-58.
 
Prymula K, Roterman I. Functional characteristics of small proteins (70 amino Acid residues) forming protein-nucleic acid complexes. J Biomol Struct Dyn 2009, 26(6):663-78.

Banach M, Roterman I. Recognition of protein-protein complexation based on hydrophobicity distribution, Bioinformation 4, 98-100, 2009

Zobnina V, Roterman I. Application of the fuzzy-oil-drop model to membrane protein simulation. Proteins 2009, 77(2):378-9
 

2008

Minervini G, Evangelista G, Polticelli F, Piwowar M, Kochańczyk M, Flis L, Malawski M, Szepieniec T, Wiśniowski Z, Matczyńska E, Prymula K,

Roterman I. Never born proteins as a test case for ab initio protein structures prediction. Bioinformation 2008, 3(4):177-9.

Brylinski M, Konieczny L, Kononowicz A, Roterman I. Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family.

J Theor Biol. 2008 Mar 21;251(2):275-85.

 

2007

Brylinski M, Konieczny L, Roterman I. Is the protein folding an aim-oriented process? Human haemoglobin as exampl, Int J. Bioinformatics and Applications 3, 234- 260 (2007)

Brylinski M, Kochanczyk M, Broniatowska E, Roterman I. Localization of ligand binding site in proteins identified in silico, J. Mol. Model 13, 665-675 (2007)

Spólnik P, Stopa B, Piekarska B, Jagusiak A, Konieczny L, Rybarska J, Król M, Roterman I, Urbanowicz B, Zieba-Palus J. The use of fibrillar, rigid Congo red nanostructures for scaffolding protein assemblies and inducing the formation of amyloid-like arrangement of molecules, Chem Biol Drug Des. 2007 Dec;70(6):491-501. Epub 2007 Nov 7.

 

2006

Bryliński M, Kochańczyk M, Konieczny L, Roterman. I, Sequence-structure-function relation characterized in silico, In Silico Biology 6, 0052 (2006)

Bryliński M, Konieczny L, Roterman I., Fuzzy-Oil-Drop Hydrophobic Force Field – A Model to Represent Late-stage Folding (In Silico) of Lysozyme. Journal of Biomolecular Structure & Dynamics, 23, 519-527, (2006).

Bryliński M, Konieczny L, Roterman I. Hydrophobic collapse in late-stage folding (in silico) of BPTI. Biochimie 88, 1229-1239 (2006)

Michał Bryliński, Leszek Konieczny, Irena Roterman. Ligation site in proteins recognized in silico. Bioinformation 1 127-129 (2006)

Konieczny L, Bryliński M, Roterman I. Gauss-Function-Based Model of Hydrophobicity Density in Proteins. In Silico Biology 6, 15-22, (2006)

Bryliński M, Konieczny L, Roterman I. Hydrophobic collapse In (In silico) protein holding, Computational Biology and Chemistry 30, 255-267 (2006)

Meus J, Bryliński M, Piwowar M, Piwowar P, Wiśniowski Z, Stefaniak J, Konieczny L, Surówka G, Roterman I. A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. Med Sci Monit, 12 BR208-214 (2006).

Piwowar M, Meus J, Piwowar P, Wiśniowski Z, Stefaniak J, Roterman I. Tandemly repeated trinucleotides – comparative analysis. Acta Biochimica Polonica. 53, 279-287 (2006).

Piekarska B, Drozd A, Konieczny L, Król K, Jurkowski W, Roterman I, Spólnik P, Stopa B, Rybarska J. The Indirect Generation of Long-distance Structural Changes in Antibodies upon their Binding to Antigen. Chem Biol Drug Des 68, 276-283, (2006)

Stopa B, Rybarska J, Drozd A, Konieczny L, Król M, Lisowski M, Piekarska B, Roterman I, Spólnik P, Zemanek G. Albumin binds self-assembling dyes as specific polymolecular ligands. Internacional Journal of Biological Macromolecules 40 , 1-8 (2006).

Król M, Roterman I, Drozd A, Konieczny L, Piekarska B, Rybarska J, Spólnik P, Stopa B. The Increased Flexibility of CDR Loops Generated in Antibodies by Congo Red Complexation Favors Antigen Binding. Journal of Biomolecular Structure & Dynamics, 23, (2006).

Spólnik P, Konieczny L, Piekarska B, Rybarska J, Stopa B, Zemanek G, Drozd A, Król M, Roterman I, Wolska-Smoleń T, Skotnicki AB. The use of the Congo red-related dye DBACR to recognize the heavy chain-derived abnormality of myeloma immunoglobulins. Arch Immunol Ther Exp (Warsz). 2006 May-Jun;54(3):217-21.

 

2005

Spólnik P, Konieczny L, Piekarska B, Rybarska J, Stopa B, Zemanek G, Drozd A, Król M, Roterman I, Wolska-Smoleń T, Skotnicki AB, 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. 2005

Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B, Spólnik P, Szneler E., An approach to understand the complexation of supramolecular dye Congo red with immunoglobulin L chain lambda. Biopolymers 77: 155-162, 2005, PMID 15641119

Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B, Spólnik P. Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction. Proteins Struct Func Bioinform 59: 545-554, 2005, PMID 15778960

Brylinski M, Konieczny L, Roterman I. Structural motifs responsible for biological function are already present in proteins during early-stage folding (in silico). MISSING 5: 227-237. 2005

Brylinski M, Konieczny L, Czerwonko P, Jurkowski W, Roterman I. Early-stage folding in proteins (in silico) - sequence to structure relation.  J Biomed Biotechnol 2: 65-79, 2005

 

2004

Bryliński M, Jurkowski W, Konieczny L, Roterman I. Early stage of protein folding simulation, Bioinformatics 2004, 20, 199-205

Brylinski M, Konieczny L, Roterman I. SPI – Structure Predictability Index for protein sequences.In Silico Biology 4: 0022. (2004)

Jurkowski W, Brylinski M, Konieczny L, Roterman I. Lysozyme folded in silico according to the limited conformational sub-space.J of Biomol Struct Dynam 22, 2:149-157. (2004)                                                                   

Jurkowski W, Wiśniowski Z, Konieczny L, Roterman I. The conformational sub-space in simulation of early-stage protein folding, Proteins: Structure, Function and Bioinformatics – 2004, 55, 115-127     

Król M, Borowski T, Roterman I, Piekarska B, Stopa B, Rybarska J, Konieczny L. Force-field parametrization and molecular dynamics simulations of Congo red. Journal of Computer Aided Molecular Design 2004, 18, 41-53                

Rybarska J, Piekarska B, Stopa B, Spólnik P, Zemanek G, Konieczny L, Roterman I. In vivo accumulation of self-assembling dye Congo red in an area marked by specific immune complexes – Possible relevance to chemotherapy Folia Histologica et Cytobiologica 2004,  42,  101-110                                 

Piekarska B, Stopa B, Konieczny L, Rybarska J, Zemanek G, Spólnik P, Roterman I, Król M. Intramolecular signaling in immunoglobulins - new evidence emerging from the use of supramolecular protein ligands. J. Physiol. Pharmacol 2004, 55, 487-501 

Spólnik P, Konieczny L, Piekarska B, Rybarska J, Stopa B, Zemanek G, Król M, Roterman I. Instability of monoclonal myeloma protein may be identified as susceptibility to penetration and binding by newly synthesized Congo red derivatives. Biochimie 2004                                                                  

 

2003

Leluk J, Konieczny L, Roterman I. Search for structural similarity in proteins, Bioinformatics  2003 19, 117-124                                                                   

Spólnik P, Piekarska B, Stopa B, Konieczny L, Zemanek G, Rybarska J, Król M, Nowak M, Roterman I. The structural abnormality of myeloma immunoglobulins tested by Congo red binding Medical Science Monitor 2003, 9, 145-153.

Król M, Roterman I, Piekarska B, Konieczny L, Rybarska J, Stopa B. Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain Biopolymers 2003, 69, 189-200                                                                       

Zemanek G, Rybarska J, Stopa B, Piekarska B, Spólnik P, Konieczny L, Roterman I, Bugajski A. Protein distorsion-derived mechanism of signal discrimination in monocytes revealed using Congo red to stain activated cells. Folia Histologica et Cytobiologica 2003, 41, 113-124                                   

Stopa B, Piekarska B, Konieczny L, Rybarska J, Spólnik P, Zemanek G, Król M, Roterman I. The structure and protein binding of amyloid-specific dye reagents Acta Biochimica Polonica 2003, 50, 1213-1227                      

Konieczny L, Roterman I. Nowotwory – struktura czy organizacja? (Cancer – structure or organization?) Menopauza – Prokreacja – Starzenie – Nowotwory 2003, 2, 87-91

 

2002

Zemanek G, Konieczny L, Piekarska B, Rybarska J, Stopa B, Spólnik P, Urbanowicz B, Nowak M, Król M, Roterman I. Egg yolk proteins from Xenopus laevis are amyloidogenic Folia Histologica et Cytobiologica  2002 40, 311-318                                 

 

2001

Roterman I, Król M, Nowak M, Konieczny L, Rybarska J, Stopa B, Piekarska B, Zemanek G. Why Congo red binding is specific for amyloid proteins Medical Science Monitor 2001, 7(4), 771-784

Konieczny L. Piekarska B, Roterman I, Rybarska J, Stopa B. Zemanek G. Przeciwciała i nośniki leków w terapii celowanej -postęp i ograniczenia Biotechnologia 2001 , 3(54), 29-36

Rybarska J, Piekarska B, Stopa B, Zemanek G, Konieczny L, Nowak M, Król M, Roterman I, Szymczakiewicz-Multanowska A Evidence that supramolecular Congo red is the sole ligation form of this dye for L chain l derived amyloid proteins Folia Histologica et Cytobiologica  2001 39, 307-314                             

Piekarska B,  Konieczny L, Rybarska J, Stopa B, Zemanek G, Szneler E, Król M, Nowak M, Roterman I. The heat induced formation of a specific binding site for self-assembled Congo red in V domain of immunoglobulin chain l  Biopolymers 2001 59, 446-456          

 

2000

Skowronek M., Roterman I., Konieczny L., Stopa B., Rybarska J., Piekarska B., Górecki A., Król M. The structure of Congo Red, Evans Blue and Trypan Blue as seen in calculation using 

different methods. Computers and Chemistry  2000, 24, 429-450

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)         

Skowronek M., Roterman I., Konieczny L., Stopa B., Rybarska J., Piekarska B., Why do Congo Red, Evans Blue and Trypan Blue differ in their complexation properties? Journal of Computational Chemistry - 2000, 21, 656-667                               

 

1999

Piekarska B, Rybarska J, Stopa B, Zemanek G, Król M, Roterman I, Konieczny L. Supramolecularity creates nonstandard ligands Acta Biochimica Polonica 1999 , 46, 841-851

 

1998

Roterman I., Rybarska J., Konieczny L., Skowronek M., Stopa B., Piekarska B. Congo Red bound to α-1-proteinase inhibitor as a model of  supra-molecular ligand and protein complex, Computers and Chemistry 1998, 22, 61-70                    

Stopa B., Górny M., Konieczny L., Piekarska B., Rybarska J., Skowronek M., Roterman I, Supramolecular ligands: Monomer structure and protein ligation capability, Biochimie 1998,  80, 963-968                                                                                      

Skowronek M, Stopa B, Konieczny L, Rybarska J, Piekarska B, Szneler E, Bakalarski G, Roterman I. Self-assembly of Congo Red – a theoretical and experimental approach to identify its supramolecular organisation in water and salt solutions , Biopolymers 1998, 46, 267-281

 

1997

Stopa B., Konieczny L., Piekarska B., Roterman I., Skowronek M. Effect of self-association of Bis-ANS and bis-azo dyes on protein binding. Biochimie, 1997, 79, 23-26                                                                              

Konieczny L., Piekarska B., Rybarska J., Skowronek M., Stopa B., Dabros W.,  Pawlicki R. Roterman I. The use of Congo Red as a lyotropic liquid crystal to carry stains in a model immunotargeting system – microscopic studies. Folia Histochemica et Cytobiologica, 1997, 35, 203-210                                     

 

1996

Konieczny L., Piekarska B., Roterman I., Rybarska J., Skowronek M., Stopa B. Perspektywy wykorzystania supramolekularnych struktur ciekłokrystalicznych do stabilizacji funkcyjnej konformacji  białek. Wiadomości Chemiczne 1996, 50, 29-42

Piekarska B., Skowronek M., Rybarska J., Stopa B., Roterman I., Konieczny L. Congo Red - stabilized intermediates in the λ light chain transition from native to molten state. Biochimie, 1996, 78, 183-189

 

1995

Rybarska J, Konieczny L, Piekarska B, Stopa B, Roterman I. The detection of specific acute phase serum protein complexes and immune complexes by Congo Red binding to serum proteins components J. Physiol. Pharmacol. 1995, 46, 221-231

Roterman I., Modelling the optimal simulation path in the peptide chain folding - Studies based on geometry of alanine heptapeptide J.Theoretical Biology 1995 177, 283-288

Roterman I, Konieczny L. Geometrical analysis of structural changes in immunoglobin domains' transition from native to molten state Computers and Chemistry 1995, 19, 204-216

Roterman I. The geometrical analysis of structural peptide backbone structure and its local deformations Biochimie 1995, 77, 204-252

 

1994

Roterman I, Konieczny L, Stopa B, Rybarska J, Piekarska B Heat induced structural changes in the Fab fragment of IgG recognised by molecular dynamics simulation - Implication for signal transduction Folia Biologica 1994, 42, 115-128

Piekarska B, Roterman I, Rybarska J, Konieczny L, Kaszuba J. The melting of native domain structure in effector activation of IgG studied by using Congo Red as a specific probe J. Physiol. Pharmacol. 1994, 45, 147-162

Konieczny L, Piekarska B, Rybarska J, Krzykwa B, Noworolski E, Pawlicki R, Roterman I. Bis azo dyes liquid crystalline micelles as possible drug carriers in immunotargeting technique J. Physiol. Pharmacol. 1994, 45, 441-454

 

1993

Roterman I. Możliwości i znaczenie techniki komputerowej w symulacji zjawisk i modelowaniu struktur biologicznych Przegląd Lekarski 1993, 50, 229-232

Roterman I, No K.T, Piekarska B, Kaszuba J, Pawlicki R, Rybarska J, Konieczny L. Bis azo dyes - Studies on the mechanism of complex formation with IgG modulated by heating or antigen binding J. Physiol. Pharmacol.1993, 3, 213-232

Kaszuba J, Konieczny L, Piekarska B, Roterman I, Rybarska J. Bis-azo dyes interference with effector activation of antibodies J. Physiol. Pharmacol. 1993, 3, 233-242

 

1991

Rybarska J, Konieczny L, Roterman I, Piekarska B. The effect of azo dyes on the formation of immune complexes Archiv. Immunol.T ther. Exp. 1991, 39, 317-327

 

1989

Roterman I, Lambert M, Gibson K, Scheraga H. 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. Dynamics 1989, 7 421-453

Roterman I, Gibson K, Scheraga H. 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. Dynamics 1989, 7, 391-419

 

1987

Rybarska J, Piekarska B, Konieczny L, Roterman I. The formation of soluble heat IgG aggregates for immunological studies  Archiv Immunol. Ther. Exp. 1987, 36, 609-622

Roterman I, Konieczny L, Bobrzecka K, Rybarska J, Ochalska B. The structure of hinge region in Fab-Fc recombinant immunoglobulins and its relation to the effector activity of these molecules  Archiv.Immunol. Therap. Exp. 1987, 35, 257-266

Bobrowski A, Roterman I, Resolution of the polarographic methods. III Resolution of linear potential sweep voltamperometry, Chemia Analityczna 1986, 31, 167-183

Jurka J, Kołosza Z, Roterman I., Globular proteins, GU wobbling, and the evolution of the genetic code, J. Mol. Evol. 1982, 19, 20-27

Górniak A, Brongel L, Jarzynowski W, Roterman I. Obrażenia wielomiejscowe niekomunikacyjne Polski Przegląd Chirurgiczny 1982, 54, 631-637

Górniak A, Brongel L, Wyroba A, Roterman I., Komunikacyjne obrażenia wielomiejscowe, Polski Przegląd Chirurgiczny 1981, 53, 145-151

 

1979

Żak Z, Małkiewicz I, Pytasz G, Riboflavin-apoprotein interaction studied by infrared and Raman spectroscopy Proceedings of an International Meeting on Flavins and Flavoproteins Flavins abd Flavoproteins Physicichemical Properties  Warsaw-Cracow 1979, 39-50

 

 

 

BOOKS

 

2013

 



Roterman I.,
Konieczny L., Banach M., Marchewka D., Kalinowska B., Baster Z., Tomanek M., and Piwowar M., Simulation of the Protein Folding Process, pp. 599-638.In: Liwo Adam Ed., Computational methods to study the structure and dynamics of biomolecules and biomolecular processes – From bioinformatics to molecular quantum mechanics. Springer Series in Bio-/Neuroinformatics, 2013

 

 

SPRINGER - Focus on Structural Biology - Volume 8 2013

Identification of Ligand Binding Site and Protein-

Protein Interaction Area

Editor: Irena Roterman-Konieczna

ISBN: 978-94-007-5284-9 (Print) 978-94-007-5285-6 (Online)

Chapter 3

Can the structure of the hydrophobic core determine the complexation site ?

Banach M, Konieczny L, Roterman I.

Chapter 4

Comparative analysis of techniques oriented on the recognition of ligand binding area in proteins.

Alejster P, Banach M, Jurkowski W, Marchewka D, Roterman I.

Chapter 6

Prediction of protein-protein binding interfaces

Marchewka D, Jurkowski W, Banach M, Roterman I.

Springer Series in Bio-/Neuroinformatics , Vol. 1

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - from Bioinformatics to Molecular Quantum Mechanics

Editor: Liwo Adam

2013 ISBN 978-3-642-28553-0

SIMULATION OF THE PROTEIN FOLDING PROCESS RATHER THAN PROTEIN STRUCTURE PREDICTION

Roterman I, Konieczny L, Banach M, Marchewka D, Kalinowska B, Baster Z, Tomanek M, Piwowar M.

 

2012

Examining protein folding process simulation and searching for common structure motifs in a protein family as experiments in the GridSpace2 Virtual
Laboratory.

Jadczyk T, Malawski M, Bubak M, Roterman I.
pp. 2520265.
In: Building a National Distributed e-Infrastructure – PL – Grid
Editors: Marian Bubak, Tomasz Szepieniec, Kazimierz Wiatr
Springer 2012

 

Woodhead Publishing Series in Biomedicine No. 22
Protein folding in silico: Protein folding versus protein structure prediction
Editor: I Roterman-Konieczna, JagiellonianUniversityMedicalCollege
ISBN 1 907568 17 4 ISBN-13: 978 1 907568 17 6

Chapter 1

The early-stage intermediate W. Jurkowski, Z. Baster, D. Dułak, and I. Roterman-Konieczna

Chapter 2

The late-stage intermediate M. Banach, L. Konieczny, and I. Roterman-Konieczna

Chapter 3

Structural information involved in the interpretation of the stepwise protein folding process P. Alejster, W. Jurkowski, and I. Roterman-Konieczna

Chapter 4

The divergence entropy characterizing the internal force field in proteins M. Banach, D. Marchewka, M. Piwowar, and I. Roterman-Konieczna

Chapter 5

Ligand-binding-site recognition M. Banach, L. Konieczny, and I. Roterman-Konieczna

Chapter 6

Use of the “fuzzy oil drop” model to identify the complexation area in protein homodimers M. Banach, L. Konieczny, and I. Roterman-Konieczna

Chapter 7

Simulation of the polypeptide chain folding process using the “fuzzy oil drop” model
L. Konieczny and I. Roterman-Konieczna

Chapter 8

Misfolded proteins M. Król, L. Konieczny, K. Stapor, Z. Wis´ niowski, W. Ziajka, G. Szoniec, and I. Roterman-Konieczna

Chapter 9

A short description of other selected ab initio methods for protein structure prediction
I. Roterman-Konieczna

Chapter 10

Conclusion L. Konieczny and I. Roterman-Konieczna