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Journal Articles
- 2024
[j91]Irena Roterman
, Leszek Konieczny, Katarzyna Stapor:
The outer-membrane componentof the multi-drug efflux system -a structural analysis based onhydrophobicity distribution. Bio Algorithms Med Syst. 20(1): 1-14 (2024)- 2023
- [j90]Irena Roterman, Katarzyna Stapor, Leszek Konieczny:
Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone. BMC Bioinform. 24(1): 418 (2023) - [j89]Irena Roterman, Katarzyna Stapor, Leszek Konieczny:
Role of environmental specificity in CASP results. BMC Bioinform. 24(1): 425 (2023) - [j88]Irena Roterman, Leszek Konieczny:
Protein Is an Intelligent Micelle. Entropy 25(6): 850 (2023) - 2022
- [j87]Katarzyna Stapor, Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman:
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. BMC Bioinform. 23(1): 100 (2022) - 2021
- [j86]Mateusz Banach, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny, Irena Roterman:
Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin. Entropy 23(4): 458 (2021) - [j85]Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman-Konieczna, Katarzyna Stapor:
ProteinUnet - An efficient alternative to SPIDER3-single for sequence-based prediction of protein secondary structures. J. Comput. Chem. 42(1): 50-59 (2021) - 2020
- [j84]Irena Roterman, Leszek Konieczny:
Protein folding vs. COVID-19 and the Mediterranean diet. Bio Algorithms Med Syst. 16(2) (2020) - [j83]Krzysztof Mikuta, Leszek Konieczny, Irena Roterman:
System to simulate the activity of living organism - construction of proteome. J. Comput. Sci. 45: 101195 (2020) - [j82]Piotr Fabian, Katarzyna Stapor, Mateusz Banach, Magdalena Ptak-Kaczor, Leszek Konieczny, Irena Roterman:
Alternative Hydrophobic Core in Proteins - The Effect of Specific Synergy. Symmetry 12(2): 273 (2020) - [j81]Mateusz Banach, Piotr Fabian, Katarzyna Stapor, Leszek Konieczny, Magdalena Ptak-Kaczor, Irena Roterman:
The Status of Edge Strands in Ferredoxin-Like Fold. Symmetry 12(6): 1032 (2020) - 2019
- [j80]Mateusz Banach, Zdzislaw Wisniowski, Magdalena Ptak, Irena Roterman:
Aggregation-promoting conditions necessary to create the complexes by acylphosphatase from the hyperthermophile Sulfolobus solfataricus. Bio Algorithms Med Syst. 15(2) (2019) - [j79]Irena Roterman, Leszek Konieczny:
The living organism: evolutionary design or an accident. Bio Algorithms Med Syst. 15(3) (2019) - [j78]Leszek Konieczny, Irena Roterman:
Personalized precision medicine. Bio Algorithms Med Syst. 15(4) (2019) - [j77]Tomasz Smolarczyk, Katarzyna Stapor, Irena Roterman-Konieczna:
Backbone dihedral angles prediction servers for protein early-stage structure prediction. Bio Algorithms Med Syst. 15(4) (2019) - [j76]Irena Roterman, Dawid Dulak, Malgorzata Gadzala, Mateusz Banach, Leszek Konieczny:
Structural analysis of the Aβ(11-42) amyloid fibril based on hydrophobicity distribution. J. Comput. Aided Mol. Des. 33(7): 665-675 (2019) - [j75]Mateusz Banach, Leszek Konieczny, Irena Roterman:
Symmetry and Dissymmetry in Protein Structure - System-Coding Its Biological Specificity. Symmetry 11(10): 1215 (2019) - 2018
- [j74]Grazyna Drabik, Jolanta Kaszuba-Zwoinska, Zdzislaw Wisniowski, Leszek Konieczny, Irena Roterman:
Chromatin 3D - will it make understanding of cancer transformation finally possible? Bio Algorithms Med Syst. 14(1) (2018) - [j73]Dawid Dulak, Mateusz Banach, Zdzislaw Wisniowski, Leszek Konieczny, Irena Roterman:
Comparison of the structure of Aβ(1-40) amyloid with the one in complex with polyphenol ε-viniferin glucoside (EVG). Bio Algorithms Med Syst. 14(2) (2018) - [j72]Mateusz Banach, Leszek Konieczny, Zdzislaw Wisniowski, Irena Roterman:
Fragment Aβ(18-41) presented within the CDR3 loop region of a shark immunoglobulin new antigen receptor single-variable domain antibody analyzed based on the fuzzy oil drop model. Bio Algorithms Med Syst. 14(3) (2018) - 2017
- [j71]Mateusz Banach, Leszek Konieczny, Zdzislaw Wisniowski, Irena Roterman:
Structure of hydrophobic core in plant carboxylesterase. Bio Algorithms Med Syst. 13(1): 13-16 (2017) - [j70]Mateusz Banach, Zdzislaw Wisniowski, Barbara Kalinowska, Leszek Konieczny, Irena Roterman:
The variability of protein structure with respect to the hydrophobic core. Bio Algorithms Med Syst. 13(2): 63 (2017) - [j69]Monika Piwowar, Ewa Matczynska, Maciej Malawski, Tomasz Szepieniec, Irena Roterman-Konieczna:
Genetic traces of never born proteins. Bio Algorithms Med Syst. 13(2): 79 (2017) - [j68]Maria Golda, Mateusz Banach, Zdzislaw Wisniowski, Wojciech Ziajka, Leszek Konieczny, Irena Roterman:
Role of the hydrophobic core in cytoskeleton protein: cardiac myosin binding protein C. Bio Algorithms Med Syst. 13(3): 161-165 (2017) - [j67]Dawid Dulak, Mateusz Banach, Zdzislaw Wisniowski, Leszek Konieczny, Irena Roterman:
Mechanism of ligand binding - PDZ domain taken as example. Bio Algorithms Med Syst. 13(4): 175-178 (2017) - [j66]Magdalena Ptak, Mateusz Banach, Zdzislaw Wisniowski, Leszek Konieczny, Irena Roterman:
Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure. Bio Algorithms Med Syst. 13(4): 179-185 (2017) - [j65]Irena Roterman, Mateusz Banach, Leszek Konieczny:
Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. Entropy 19(4): 167 (2017) - 2016
- [j64]Mateusz Banach, Leszek Konieczny, Irena Roterman:
Dissimilar sequence: similar structure of proteins. Bio Algorithms Med Syst. 12(3): 117-121 (2016) - [j63]Mateusz Banach, Barbara Kalinowska, Leszek Konieczny, Irena Roterman:
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 (2016) - [j62]Irena Roterman, Mateusz Banach, Barbara Kalinowska, Leszek Konieczny:
Influence of the Aqueous Environment on Protein Structure - A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis. Entropy 18(10): 351 (2016) - 2015
- [j61]Katarzyna Chlopas, Anna Jagusiak, Leszek Konieczny, Barbara Piekarska, Irena Roterman, Janina Rybarska, Barbara Stopa, Grzegorz Zemanek, Elzbieta Bielanska, Piotr Piwowar, Krystyna Sadlik:
The use of Titan yellow dye as a metal ion binding marker for studies on the formation of specific complexes by supramolecular Congo red. Bio Algorithms Med Syst. 11(1): 9-17 (2015) - [j60]Irena Roterman-Konieczna, Piotr Fabian, Katarzyna Stapor:
A method of predicting the secondary protein structure based on dictionaries. Bio Algorithms Med Syst. 11(3): 163-170 (2015) - [j59]Roksana Rosicka, Mateusz Banach, Irena Roterman-Konieczna:
Application of divergence entropy to characterize the structure of lipid-binding proteins. Bio Algorithms Med Syst. 11(3): 171-176 (2015) - [j58]Irena Roterman-Konieczna, Mateusz Banach, Leszek Konieczny:
Hydrophobic core structure of macromomycin - the apoprotein of the antitumor antibiotic auromomycin - fuzzy oil drop model applied. Bio Algorithms Med Syst. 11(3): 177-181 (2015) - [j57]Barbara Kalinowska, Mateusz Banach, Leszek Konieczny, Irena Roterman:
Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins. Entropy 17(3): 1477-1507 (2015) - [j56]Barbara Kalinowska, Piotr Fabian, Katarzyna Stapor, Irena Roterman:
Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding. J. Comput. Aided Mol. Des. 29(7): 609-618 (2015) - 2014
- [j55]Kinga Salapa, Agata Trawinska, Irena Roterman, Ryszard Tadeusiewicz:
Speaker identification based on artificial neural networks. Case study: the Polish vowel (pilot study). Bio Algorithms Med Syst. 10(2): 91-99 (2014) - [j54]Monika Piwowar, Jacek Dygut, Piotr Piwowar, Leszek Konieczny, Irena Roterman:
Attempt at a systemic outlook on aging and carcinogenesis. Bio Algorithms Med Syst. 10(3): 101-115 (2014) - [j53]Jacek Dygut, Sylwia Plonka, Irena Roterman-Konieczna:
Involvement of medical experts in legal proceedings: an e-learning approach. Bio Algorithms Med Syst. 10(3): 159-165 (2014) - 2013
- [j52]Monika Piwowar, Mateusz Banach, Leszek Konieczny, Jacques Chomilier, Irena Roterman:
Structural role of exons in hemoglobin. Bio Algorithms Med Syst. 9(2): 81-90 (2013) - [j51]Monika Piwowar, Mateusz Banach, Leszek Konieczny, Irena Roterman:
Structural role of exon-coded fragments in proteins. Bio Algorithms Med Syst. 9(3): 103-114 (2013) - [j50]Ilona Laskowska, Ludmila Zajac-Lamparska, Monika Wilkosc, Michal Malicki, Agnieszka Szalkowska, Anna Jurgielewicz, Pawel Lewandowski, Pawel Wegrzyn, Irena Roterman-Konieczna, Pawel Izdebski:
A serious game - a new training addressing particularly prospective memory in the elderly. Bio Algorithms Med Syst. 9(3): 155-165 (2013) - [j49]Kinga Salapa, Agata Trawinska, Irena Roterman-Konieczna:
Forensic voice comparison by means of artificial neural networks. Bio Algorithms Med Syst. 9(4): 191-197 (2013) - 2012
- [j48]Leszek Konieczny, Mateusz Banach, Irena Roterman:
Stability of Two Natural Homologous Proteins with Different Folds. Bio Algorithms Med Syst. 8(2): 185-193 (2012) - [j47]Kinga Salapa, Barbara Kalinowska, Tomasz Jadczyk, Irena Roterman:
Measurement of Hydrophobicity Distribution in Proteins - Complete Redundant Protein Data Bank. Bio Algorithms Med Syst. 8(2): 195-206 (2012) - [j46]Pawel Spólnik, Leszek Konieczny, Irena Roterman, Michal Markiewicz:
BIOLOGICAL CLOCK - Is the Need for a Clock a Common Issue for Cells and Computers? Bio Algorithms Med Syst. 8(2): 255-265 (2012) - [j45]Kinga Salapa, Barbara Kalinowska, Tomasz Jadczyk, Irena Roterman:
Measurement of Hydrophobicity Distribution in Proteins - Non-redundant Protein Data Bank. Bio Algorithms Med Syst. 8(3): 327-338 (2012) - [j44]Leszek Konieczny, Michal Markiewicz, Piotr Piwowar, Irena Roterman:
Technical Solutions for Bio-Measurements. Bio Algorithms Med Syst. 8(4): 339-349 (2012) - [j43]Damian Marchewka, Irena Roterman, Magdalena Strus, Klaudyna Spiewak, Grzegorz Majka:
Structural Analysis of the Lactoferrin Iron Binding Pockets. Bio Algorithms Med Syst. 8(4): 351-359 (2012) - [j42]Eryk Ciepiela, Tomasz Jadczyk, Daniel Harezlak, Marek Kasztelnik, Piotr Nowakowski, Grzegorz Dyk, Maciej Malawski, Marian Bubak, Irena Roterman:
Computations of Protein Hydrophobicity Profile as Virtual Experiment in Gridspace Virtual Laboratory. Bio Algorithms Med Syst. 8(4): 361-372 (2012) - [j41]Wieslaw Chmielnicki, Irena Roterman-Konieczna, Katarzyna Stapor:
An improved protein fold recognition with support vector machines. Expert Syst. J. Knowl. Eng. 29(2): 200-211 (2012) - 2011
- [j40]Giuseppe Evangelista, Giovanni Minervini, Fabio Polticelli, Maciej Malawski, Tomasz Szepieniec, Lukasz Flis, Katarzyna Prymula, Marek Kochanczyk, Ewa Matczynska, Zdzislaw Wisniowski, Kinga Salapa, Mateusz Banach, Irena Roterman:
Ab initio protein structure prediction - the hydrophobicity distribution analysis. Bio Algorithms Med Syst. 7(2): 5-12 (2011) - [j39]Katarzyna Prymula, Tomasz Jadczyk, Irena Roterman:
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. J. Comput. Aided Mol. Des. 25(2): 117-133 (2011) - 2010
- [j38]Irena Roterman-Konieczna:
Editorial note. Bio Algorithms Med Syst. 6(12-S): 13 (2010) - [j37]Marek Ksiezyk, Jan Trabka, Andrzej Zarnecki, Ryszard Tadeusiewicz, Irena Roterman:
Forty years of medical informatics in Medical Academy (currently) Jagiellonian University - Medical College (JU CM). Bio Algorithms Med Syst. 6(12-S): 27-28 (2010) - [j36]Mateusz Banach, Irena Roterman:
Identification of protein-protein complexation area. Bio Algorithms Med Syst. 6(12-S): 41-42 (2010) - [j35]Piotr Marek, Irena Roterman:
Internal force field in protein molecule. Bio Algorithms Med Syst. 6(12-S): 123-124 (2010) - [j34]Wiktor Pilat, Irena Roterman:
In silico "Game" between the patient and his/her disease. Bio Algorithms Med Syst. 6(12-S): 159-160 (2010) - [j33]Lukasz Proszek, Irena Roterman:
Automatic Classification of Protein Structures based on Genetic Algorithm alignment of the Hydrophobicity Difference Profiles obtained from the Fuzzy Oil Drop Model. Bio Algorithms Med Syst. 6(12-S): 173-174 (2010) - 2009
- [j32]Andrzej A. Kononowicz, Irena Roterman:
Chemical pathways - visualisation of classical analytical procedures in chemistry by the use of flow charts. Bio Algorithms Med Syst. 5(9): 121-126 (2009) - [j31]Dorota Gorzelany, Jerzy Walocha, Anna Wojas-Pelc, Wladyslaw Lejman, Ryszard Gryglewski, Wieslaw Pyrczak, Irena Roterman:
Male portrait head. Bio Algorithms Med Syst. 5(9): 137-141 (2009) - [j30]Irena Roterman:
The XV century patients (as presented on Wit Stwosz altar) diagnozed. Bio Algorithms Med Syst. 5(9): 147-152 (2009) - [j29]Piotr Kielkowicz, Irena Roterman:
Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate. Bio Algorithms Med Syst. 5(10): 15-23 (2009) - [j28]Katarzyna Prymula, Irena Roterman:
Structural Entropy to Characterize Small Proteins (70 aa) and Their Interactions. Entropy 11(1): 62-84 (2009) - 2008
- [j27]Damian Marchewka, Irena Roterman:
Ligands database. Bio Algorithms Med Syst. 4(8): 15-18 (2008) - [j26]Grzegorz Porebski, Piotr Obtulowicz, Monika Piwowar, Irena Roterman-Konieczna:
Association between the N-acetylation genetic polymorphism and aspirin-induced urticartia. Bio Algorithms Med Syst. 4(8): 19-23 (2008) - [j25]Piotr Walecki, Wojciech Lason, Edward Jacek Gorzelanczyk, Irena Roterman:
The influence of coffee on an eyeball movement. Bio Algorithms Med Syst. 4(8): 69-72 (2008) - [j24]Piotr Walecki, Wojciech Lason, Irena Roterman-Konieczna:
Advanced measurement of saccadic eye movements - study of invariable and significant physiological features. Bio Algorithms Med Syst. 4(8): 81-92 (2008) - 2007
- [j23]Maciej Malawski, Tomasz Szepieniec, Marek Kochanczyk, Monika Piwowar, Irena Roterman:
An approach to protein folding on the grid - EUChinaGrid experience. Bio Algorithms Med Syst. 3(5): 45-49 (2007) - [j22]Monika Piwowar, Tomasz Szepieniec, Irena Roterman:
Massive identification of similarities in DNA materials organized in Grid environment. Bio Algorithms Med Syst. 3(5): 51-52 (2007) - [j21]Irena Roterman-Konieczna:
Mathematical Oncology - What is it? Bio Algorithms Med Syst. 3(6): 37-39 (2007) - [j20]Michal Brylinski, Leszek Konieczny, Irena Roterman:
Is the protein folding an aim-oriented process? Human haemoglobin as example. Int. J. Bioinform. Res. Appl. 3(2): 234-260 (2007) - [j19]Michal Brylinski, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochanczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman:
Prediction of Functional Sites Based on the Fuzzy Oil Drop Model. PLoS Comput. Biol. 3(5) (2007) - 2006
- [j18]Joanna Grabska-Chrzastowska, Anna Drozd, Leszek Konieczny, Janina Rybarska, Barbara Stopa, Barbara Piekarska, Irena Roterman, Marcin Król, Pawel Spólnik, Grzegorz Zemanek:
Specific supramolecular ligands with proteins. Possible practical application. Bio Algorithms Med Syst. 1(1-2): 113-116 (2006) - [j17]Joanna Rybarska, Pawel Spólnik, Anna Drozd, Leszek Konieczny, Barbara Piekarska, Barbara Stopa, Grzegorz Zemanek, Marcin Król, Irena Roterman-Konieczna:
Protein complexes with supramolecular ligands formed and revealed in two-dimensional electrophoresis. The search for computer analysis of results. Bio Algorithms Med Syst. 1(1-2): 133-138 (2006) - [j16]Andrzej Konowicz, Marta Zabinska-Popiela, Irena Roterman-Konieczna, Jozef Krzysiek:
A multi-path computer-based examination system for students of medicine. Bio Algorithms Med Syst. 1(1-2): 165-170 (2006) - [j15]Krzysztof Sarapata, Grzegorz Bilo, Wieslaw Pyrczak, Andrzej A. Kononowicz, Irena Roterman-Konieczna, Kalina Kawecka-Jaszcz:
Application of cryptography in cardiologic teleconsultation. Bio Algorithms Med Syst. 1(1-2): 365-368 (2006) - [j14]Maciej Malawski, Tomasz Szepieniec, Irena Roterman-Konieczna:
Grid systems and their applications to biomedical science. Bio Algorithms Med Syst. 2(3): 43-46 (2006) - [j13]Andrzej A. Kononowicz, Irena Roterman-Konieczna:
E-learning as a new tool in medicine teaching on the example of an introductory statistics course. Bio Algorithms Med Syst. 2(3): 61-65 (2006) - [j12]Elzbieta Broniatowska, Olga Stepien, Irena Roterman:
The ligand database server. Bio Algorithms Med Syst. 2(4): 21-24 (2006) - [j11]Michal Brylinski, Leszek Konieczny, Irena Roterman:
Hydrophobic collapse in (in silico) protein folding. Comput. Biol. Chem. 30(4): 255-267 (2006) - [j10]Leszek Konieczny, Michal Brylinski, Irena Roterman:
Gauss-Function-Based Model of Hydrophobicity Density in Proteins. Silico Biol. 6(1-2): 15-22 (2006) - [j9]Michal Brylinski, Marek Kochanczyk, Leszek Konieczny, Irena Roterman:
Sequence-Structure-Function Relation Characterized in silico. Silico Biol. 6(6): 589-600 (2006) - 2004
- [j8]Michal Brylinski, Wiktor Jurkowski, Leszek Konieczny, Irena Roterman:
Limited conformational space for early-stage protein folding simulation. Bioinform. 20(2): 199-205 (2004) - [j7]Michal Brylinski, Leszek Konieczny, Irena Roterman:
SPI - Structure predictability index for protein sequences. Silico Biol. 5(3): 227-237 (2004) - [j6]Marcin Król, Tomasz Borowski, Irena Roterman, Barbara Piekarska, Barbara Stopa, Joanna Rybarska, Leszek Konieczny:
Force-field parametrization and molecular dynamics simulations of Congo red. J. Comput. Aided Mol. Des. 18(1): 41-53 (2004) - 2003
- [j5]Jacek Leluk, Leszek Konieczny, Irena Roterman:
Search for structural similarity in proteins. Bioinform. 19(1): 117-124 (2003) - 2000
- [j4]Marek Skowronek, Irena Roterman, Leszek Konieczny, Barbara Stopa, Janina Rybarska, Barbara Piekarska, Andrzej Górecki, Marek Król:
The Conformational Characteristics of Congo Red, Evans Blue and Trypan Blue. Comput. Chem. 24(3-4): 429-450 (2000) - [j3]Marek Skowronek, Irena Roterman, Leszek Konieczny, Barbara Stopa, Janina Rybarska, Barbara Piekarska:
Why do Congo Red, Evans Blue, and Trypan Blue differ in their complexation properties? J. Comput. Chem. 21(8): 656-667 (2000) - 1998
- [j2]Irena Roterman, Janina Rybarska, Leszek Konieczny, Marek Skowronek, Barbara Stopa, Barbara Piekarska, Grzegorz Bakalarski:
Congo Red Bound to -1-Proteinase Inhibitor As a Model of Supramolecular Ligand and Protein Complex. Comput. Chem. 22(1): 61-70 (1998) - 1995
- [j1]Irena Roterman, Leszek Konieczny:
Geometrical Analysis of Structural Changes in Immunoglobulin Domains' Transition From Native to Molten State. Comput. Chem. 19(3): 247-252 (1995)
Conference and Workshop Papers
- 2010
- [c1]Wieslaw Chmielnicki, Katarzyna Stapor, Irena Roterman-Konieczna:
An Efficient Multi-class Support Vector Machine Classifier for Protein Fold Recognition. IWPACBB 2010: 77-84
Parts in Books or Collections
- 2019
- [p2]Katarzyna Stapor, Irena Roterman-Konieczna, Piotr Fabian:
Machine Learning Methods for the Protein Fold Recognition Problem. Machine Learning Paradigms 2019: 101-127 - 2012
- [p1]Tomasz Jadczyk, Maciej Malawski, Marian Bubak, Irena Roterman:
Examining Protein Folding Process Simulation and Searching for Common Structure Motifs in a Protein Family as Experiments in the GridSpace2 Virtual Laboratory. PL-Grid 2012: 252-264
Informal and Other Publications
- 2024
- [i1]Krzysztof Kotowski, Irena Roterman, Katarzyna Stapor:
Protein intrinsic disorder prediction using Attention U-Net and ProtTrans protein language model. CoRR abs/2404.08108 (2024)
Coauthor Index
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