Geometrical Analysis of Structural Changes in Immunoglobulin Domains' Transition From Native to Molten State. - Irena Roterman; Leszek Konieczny (Comput. Chem., 1995)

Congo Red Bound to -1-Proteinase Inhibitor As a Model of Supramolecular Ligand and Protein Complex. - Irena Roterman; Janina Rybarska; Leszek Konieczny; Marek Skowronek; Barbara Stopa; Barbara Piekarska; Grzegorz Bakalarski (Comput. Chem., 1998)

The Conformational Characteristics of Congo Red, Evans Blue and Trypan Blue. - Marek Skowronek; Irena Roterman; Leszek Konieczny; Barbara Stopa; Janina Rybarska; Barbara Piekarska; Andrzej Górecki; Marek Król (Comput. Chem., 2000)

Why do Congo Red, Evans Blue, and Trypan Blue differ in their complexation properties? - Marek Skowronek; Irena Roterman; Leszek Konieczny; Barbara Stopa; Janina Rybarska; Barbara Piekarska (J. Comput. Chem., 2000)

Search for structural similarity in proteins. - Jacek Leluk; Leszek Konieczny; Irena Roterman (Bioinform., 2003)

Limited conformational space for early-stage protein folding simulation. - Michal Brylinski; Wiktor Jurkowski; Leszek Konieczny; Irena Roterman (Bioinform., 2004)

SPI - Structure predictability index for protein sequences. - Michal Brylinski; Leszek Konieczny; Irena Roterman (Silico Biol., 2004)

Force-field parametrization and molecular dynamics simulations of Congo red. - Marcin Król; Tomasz Borowski; Irena Roterman; Barbara Piekarska; Barbara Stopa; Joanna Rybarska; Leszek Konieczny (J. Comput. Aided Mol. Des., 2004)

The ligand database server. - Elzbieta Broniatowska; Olga Stepien; Irena Roterman (Bio Algorithms Med Syst., 2006)

Specific supramolecular ligands with proteins. Possible practical application. - Joanna Grabska-Chrzastowska; Anna Drozd; Leszek Konieczny; Janina Rybarska; Barbara Stopa; Barbara Piekarska; Irena Roterman; Marcin Król; Pawel Spólnik; Grzegorz Zemanek (Bio Algorithms Med Syst., 2006)

E-learning as a new tool in medicine teaching on the example of an introductory statistics course. - Andrzej A. Kononowicz; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2006)

A multi-path computer-based examination system for students of medicine. - Andrzej Konowicz; Marta Zabinska-Popiela; Irena Roterman-Konieczna; Jozef Krzysiek (Bio Algorithms Med Syst., 2006)

Grid systems and their applications to biomedical science. - Maciej Malawski; Tomasz Szepieniec; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2006)

Protein complexes with supramolecular ligands formed and revealed in two-dimensional electrophoresis. The search for computer analysis of results. - Joanna Rybarska; Pawel Spólnik; Anna Drozd; Leszek Konieczny; Barbara Piekarska; Barbara Stopa; Grzegorz Zemanek; Marcin Król; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2006)

Application of cryptography in cardiologic teleconsultation. - Krzysztof Sarapata; Grzegorz Bilo; Wieslaw Pyrczak; Andrzej A. Kononowicz; Irena Roterman-Konieczna; Kalina Kawecka-Jaszcz (Bio Algorithms Med Syst., 2006)

Hydrophobic collapse in (in silico) protein folding. - Michal Brylinski; Leszek Konieczny; Irena Roterman (Comput. Biol. Chem., 2006)

Sequence-Structure-Function Relation Characterized in silico. - Michal Brylinski; Marek Kochanczyk; Leszek Konieczny; Irena Roterman (Silico Biol., 2006)

Gauss-Function-Based Model of Hydrophobicity Density in Proteins. - Leszek Konieczny; Michal Brylinski; Irena Roterman (Silico Biol., 2006)

An approach to protein folding on the grid - EUChinaGrid experience. - Maciej Malawski; Tomasz Szepieniec; Marek Kochanczyk; Monika Piwowar; Irena Roterman (Bio Algorithms Med Syst., 2007)

Massive identification of similarities in DNA materials organized in Grid environment. - Monika Piwowar; Tomasz Szepieniec; Irena Roterman (Bio Algorithms Med Syst., 2007)

Mathematical Oncology - What is it? - Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2007)

Is the protein folding an aim-oriented process? Human haemoglobin as example. - Michal Brylinski; Leszek Konieczny; Irena Roterman (Int. J. Bioinform. Res. Appl., 2007)

Prediction of Functional Sites Based on the Fuzzy Oil Drop Model. - Michal Brylinski; Katarzyna Prymula; Wiktor Jurkowski; Marek Kochanczyk; Ewa Stawowczyk; Leszek Konieczny; Irena Roterman (PLoS Comput. Biol., 2007)

Ligands database. - Damian Marchewka; Irena Roterman (Bio Algorithms Med Syst., 2008)

Association between the N-acetylation genetic polymorphism and aspirin-induced urticartia. - Grzegorz Porebski; Piotr Obtulowicz; Monika Piwowar; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2008)

The influence of coffee on an eyeball movement. - Piotr Walecki; Wojciech Lason; Edward Jacek Gorzelanczyk; Irena Roterman (Bio Algorithms Med Syst., 2008)

Advanced measurement of saccadic eye movements - study of invariable and significant physiological features. - Piotr Walecki; Wojciech Lason; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2008)

Male portrait head. - Dorota Gorzelany; Jerzy Walocha; Anna Wojas-Pelc; Wladyslaw Lejman; Ryszard Gryglewski; Wieslaw Pyrczak; Irena Roterman (Bio Algorithms Med Syst., 2009)

Unfolding simulation to verify the concept of limited conformational sub-space for early-stage intermediate. - Piotr Kielkowicz; Irena Roterman (Bio Algorithms Med Syst., 2009)

Chemical pathways - visualisation of classical analytical procedures in chemistry by the use of flow charts. - Andrzej A. Kononowicz; Irena Roterman (Bio Algorithms Med Syst., 2009)

The XV century patients (as presented on Wit Stwosz altar) diagnozed. - Irena Roterman (Bio Algorithms Med Syst., 2009)

Structural Entropy to Characterize Small Proteins (70 aa) and Their Interactions. - Katarzyna Prymula; Irena Roterman (Entropy, 2009)

An Efficient Multi-class Support Vector Machine Classifier for Protein Fold Recognition. - Wieslaw Chmielnicki; Katarzyna Stapor; Irena Roterman-Konieczna (IWPACBB, 2010)

Identification of protein-protein complexation area. - Mateusz Banach; Irena Roterman (Bio Algorithms Med Syst., 2010)

Forty years of medical informatics in Medical Academy (currently) Jagiellonian University - Medical College (JU CM). - Marek Ksiezyk; Jan Trabka; Andrzej Zarnecki; Ryszard Tadeusiewicz; Irena Roterman (Bio Algorithms Med Syst., 2010)

Internal force field in protein molecule. - Piotr Marek; Irena Roterman (Bio Algorithms Med Syst., 2010)

In silico "Game" between the patient and his/her disease. - Wiktor Pilat; Irena Roterman (Bio Algorithms Med Syst., 2010)

Automatic Classification of Protein Structures based on Genetic Algorithm alignment of the Hydrophobicity Difference Profiles obtained from the Fuzzy Oil Drop Model. - Lukasz Proszek; Irena Roterman (Bio Algorithms Med Syst., 2010)

Editorial note. - Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2010)

Ab initio protein structure prediction - the hydrophobicity distribution analysis. - Giuseppe Evangelista; Giovanni Minervini; Fabio Polticelli; Maciej Malawski; Tomasz Szepieniec; Lukasz Flis; Katarzyna Prymula; Marek Kochanczyk; Ewa Matczynska; Zdzislaw Wisniowski; Kinga Salapa; Mateusz Banach; et al. (Bio Algorithms Med Syst., 2011)

Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. - Katarzyna Prymula; Tomasz Jadczyk; Irena Roterman (J. Comput. Aided Mol. Des., 2011)

Examining Protein Folding Process Simulation and Searching for Common Structure Motifs in a Protein Family as Experiments in the GridSpace2 Virtual Laboratory. - Tomasz Jadczyk; Maciej Malawski; Marian Bubak; Irena Roterman (PL-Grid, 2012)

Computations of Protein Hydrophobicity Profile as Virtual Experiment in Gridspace Virtual Laboratory. - Eryk Ciepiela; Tomasz Jadczyk; Daniel Harezlak; Marek Kasztelnik; Piotr Nowakowski; Grzegorz Dyk; Maciej Malawski; Marian Bubak; Irena Roterman (Bio Algorithms Med Syst., 2012)

Stability of Two Natural Homologous Proteins with Different Folds. - Leszek Konieczny; Mateusz Banach; Irena Roterman (Bio Algorithms Med Syst., 2012)

Technical Solutions for Bio-Measurements. - Leszek Konieczny; Michal Markiewicz; Piotr Piwowar; Irena Roterman (Bio Algorithms Med Syst., 2012)

Structural Analysis of the Lactoferrin Iron Binding Pockets. - Damian Marchewka; Irena Roterman; Magdalena Strus; Klaudyna Spiewak; Grzegorz Majka (Bio Algorithms Med Syst., 2012)

Measurement of Hydrophobicity Distribution in Proteins - Complete Redundant Protein Data Bank. - Kinga Salapa; Barbara Kalinowska; Tomasz Jadczyk; Irena Roterman (Bio Algorithms Med Syst., 2012)

Measurement of Hydrophobicity Distribution in Proteins - Non-redundant Protein Data Bank. - Kinga Salapa; Barbara Kalinowska; Tomasz Jadczyk; Irena Roterman (Bio Algorithms Med Syst., 2012)

BIOLOGICAL CLOCK - Is the Need for a Clock a Common Issue for Cells and Computers? - Pawel Spólnik; Leszek Konieczny; Irena Roterman; Michal Markiewicz (Bio Algorithms Med Syst., 2012)

An improved protein fold recognition with support vector machines. - Wieslaw Chmielnicki; Irena Roterman-Konieczna; Katarzyna Stapor (Expert Syst. J. Knowl. Eng., 2012)

A serious game - a new training addressing particularly prospective memory in the elderly. - Ilona Laskowska; Ludmila Zajac-Lamparska; Monika Wilkosc; Michal Malicki; Agnieszka Szalkowska; Anna Jurgielewicz; Pawel Lewandowski; Pawel Wegrzyn; Irena Roterman-Konieczna; Pawel Izdebski (Bio Algorithms Med Syst., 2013)

Structural role of exons in hemoglobin. - Monika Piwowar; Mateusz Banach; Leszek Konieczny; Jacques Chomilier; Irena Roterman (Bio Algorithms Med Syst., 2013)

Structural role of exon-coded fragments in proteins. - Monika Piwowar; Mateusz Banach; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2013)

Forensic voice comparison by means of artificial neural networks. - Kinga Salapa; Agata Trawinska; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2013)

Involvement of medical experts in legal proceedings: an e-learning approach. - Jacek Dygut; Sylwia Plonka; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2014)

Attempt at a systemic outlook on aging and carcinogenesis. - Monika Piwowar; Jacek Dygut; Piotr Piwowar; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2014)

Speaker identification based on artificial neural networks. Case study: the Polish vowel (pilot study). - Kinga Salapa; Agata Trawinska; Irena Roterman; Ryszard Tadeusiewicz (Bio Algorithms Med Syst., 2014)

The use of Titan yellow dye as a metal ion binding marker for studies on the formation of specific complexes by supramolecular Congo red. - Katarzyna Chlopas; Anna Jagusiak; Leszek Konieczny; Barbara Piekarska; Irena Roterman; Janina Rybarska; Barbara Stopa; Grzegorz Zemanek; Elzbieta Bielanska; Piotr Piwowar; Krystyna Sadlik (Bio Algorithms Med Syst., 2015)

Application of divergence entropy to characterize the structure of lipid-binding proteins. - Roksana Rosicka; Mateusz Banach; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2015)

A method of predicting the secondary protein structure based on dictionaries. - Irena Roterman-Konieczna; Piotr Fabian; Katarzyna Stapor (Bio Algorithms Med Syst., 2015)

Hydrophobic core structure of macromomycin - the apoprotein of the antitumor antibiotic auromomycin - fuzzy oil drop model applied. - Irena Roterman-Konieczna; Mateusz Banach; Leszek Konieczny (Bio Algorithms Med Syst., 2015)

Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins. - Barbara Kalinowska; Mateusz Banach; Leszek Konieczny; Irena Roterman (Entropy, 2015)

Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding. - Barbara Kalinowska; Piotr Fabian; Katarzyna Stapor; Irena Roterman (J. Comput. Aided Mol. Des., 2015)

Dissimilar sequence: similar structure of proteins. - Mateusz Banach; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2016)

Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes - An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins. - Mateusz Banach; Barbara Kalinowska; Leszek Konieczny; Irena Roterman (Entropy, 2016)

Influence of the Aqueous Environment on Protein Structure - A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis. - Irena Roterman; Mateusz Banach; Barbara Kalinowska; Leszek Konieczny (Entropy, 2016)

Structure of hydrophobic core in plant carboxylesterase. - Mateusz Banach; Leszek Konieczny; Zdzislaw Wisniowski; Irena Roterman (Bio Algorithms Med Syst., 2017)

The variability of protein structure with respect to the hydrophobic core. - Mateusz Banach; Zdzislaw Wisniowski; Barbara Kalinowska; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2017)

Mechanism of ligand binding - PDZ domain taken as example. - Dawid Dulak; Mateusz Banach; Zdzislaw Wisniowski; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2017)

Role of the hydrophobic core in cytoskeleton protein: cardiac myosin binding protein C. - Maria Golda; Mateusz Banach; Zdzislaw Wisniowski; Wojciech Ziajka; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2017)

Genetic traces of never born proteins. - Monika Piwowar; Ewa Matczynska; Maciej Malawski; Tomasz Szepieniec; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2017)

Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure. - Magdalena Ptak; Mateusz Banach; Zdzislaw Wisniowski; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2017)

Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. - Irena Roterman; Mateusz Banach; Leszek Konieczny (Entropy, 2017)

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. - Mateusz Banach; Leszek Konieczny; Zdzislaw Wisniowski; Irena Roterman (Bio Algorithms Med Syst., 2018)

Chromatin 3D - will it make understanding of cancer transformation finally possible? - Grazyna Drabik; Jolanta Kaszuba-Zwoinska; Zdzislaw Wisniowski; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2018)

Comparison of the structure of Aβ(1-40) amyloid with the one in complex with polyphenol ε-viniferin glucoside (EVG). - Dawid Dulak; Mateusz Banach; Zdzislaw Wisniowski; Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2018)

Aggregation-promoting conditions necessary to create the complexes by acylphosphatase from the hyperthermophile Sulfolobus solfataricus. - Mateusz Banach; Zdzislaw Wisniowski; Magdalena Ptak; Irena Roterman (Bio Algorithms Med Syst., 2019)

Personalized precision medicine. - Leszek Konieczny; Irena Roterman (Bio Algorithms Med Syst., 2019)

The living organism: evolutionary design or an accident. - Irena Roterman; Leszek Konieczny (Bio Algorithms Med Syst., 2019)

Backbone dihedral angles prediction servers for protein early-stage structure prediction. - Tomasz Smolarczyk; Katarzyna Stapor; Irena Roterman-Konieczna (Bio Algorithms Med Syst., 2019)

Structural analysis of the Aβ(11-42) amyloid fibril based on hydrophobicity distribution. - Irena Roterman; Dawid Dulak; Malgorzata Gadzala; Mateusz Banach; Leszek Konieczny (J. Comput. Aided Mol. Des., 2019)

Symmetry and Dissymmetry in Protein Structure - System-Coding Its Biological Specificity. - Mateusz Banach; Leszek Konieczny; Irena Roterman (Symmetry, 2019)

Machine Learning Methods for the Protein Fold Recognition Problem. - Katarzyna Stapor; Irena Roterman-Konieczna; Piotr Fabian (Machine Learning Paradigms, 2019)

Protein folding vs. COVID-19 and the Mediterranean diet. - Irena Roterman; Leszek Konieczny (Bio Algorithms Med Syst., 2020)

System to simulate the activity of living organism - construction of proteome. - Krzysztof Mikuta; Leszek Konieczny; Irena Roterman (J. Comput. Sci., 2020)

The Status of Edge Strands in Ferredoxin-Like Fold. - Mateusz Banach; Piotr Fabian; Katarzyna Stapor; Leszek Konieczny; Magdalena Ptak-Kaczor; Irena Roterman (Symmetry, 2020)

Alternative Hydrophobic Core in Proteins - The Effect of Specific Synergy. - Piotr Fabian; Katarzyna Stapor; Mateusz Banach; Magdalena Ptak-Kaczor; Leszek Konieczny; Irena Roterman (Symmetry, 2020)

Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin. - Mateusz Banach; Katarzyna Stapor; Piotr Fabian; Leszek Konieczny; Irena Roterman (Entropy, 2021)

ProteinUnet - An efficient alternative to SPIDER3-single for sequence-based prediction of protein secondary structures. - Krzysztof Kotowski; Tomasz Smolarczyk; Irena Roterman-Konieczna; Katarzyna Stapor (J. Comput. Chem., 2021)

Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. - Katarzyna Stapor; Krzysztof Kotowski; Tomasz Smolarczyk; Irena Roterman (BMC Bioinform., 2022)

Protein Is an Intelligent Micelle. - Irena Roterman; Leszek Konieczny (Entropy, 2023)

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone. - Irena Roterman; Katarzyna Stapor; Leszek Konieczny (BMC Bioinform., 2023)

Role of environmental specificity in CASP results. - Irena Roterman; Katarzyna Stapor; Leszek Konieczny (BMC Bioinform., 2023)

The outer-membrane componentof the multi-drug efflux system -a structural analysis based onhydrophobicity distribution. - Irena Roterman; Leszek Konieczny; Katarzyna Stapor (Bio Algorithms Med Syst., 2024)

Protein intrinsic disorder prediction using Attention U-Net and ProtTrans protein language model. - Krzysztof Kotowski; Irena Roterman; Katarzyna Stapor (CoRR, 2024)

DisorderUnetLM: Validating ProteinUnet for efficient protein intrinsic disorder prediction. - Krzysztof Kotowski; Irena Roterman; Katarzyna Stapor (Comput. Biol. Medicine, 2025)