Publicacions en revistes

• Overcoming flavin-driven inactivation of alcohol dehydrogenases through enzyme immobilization

  Sergio Fernando Castillo Pacheco, Katarzyna Patrycja Swiderek, Maria Jesus Moran, Ainhoa Oliden-Sanchez, Vicente Moliner Ibáñez, Luca Salassa, Fernando Lopez-Gallego. CATALYSIS SCIENCE & TECHNOLOGY. Num. 21. Vol. 15. pp. 6486-6498. 2025. Científic.

• Engineering the Tobacco Etch Virus Protease toward a Platform for Traceless Cleavage Using Distal Site Prediction and Smart Library Design

  Martijn P. Bemelmans, Bach-Ngan Wetzel, Florian G. Neusius, Florian Tieves, Christian Schwarz, Ivan Mateljak, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Miguel Alcalde, Volker Sieber. ACS Synthetic Biology. Num. 9. Vol. 14. pp. 3721-3733. 2025. Científic.

• Selective chemical recycling of polyhydroxybutyrate into high-value hydroxy acid using the taurine organocatalyst

  Elena Gabirondo, Ainhoa Maiz-Iginitz, Marta Ximenis, Katarzyna Patrycja Swiderek, Daniel Andrés-Sanz, Vicente Moliner Ibáñez, Luis Cabedo Mas, Andrea H. Westlie, Eugene Y.-X. Chen, Daniel Alonso Cerrón-Infantes, Miriam M. Unterlass, Fernando López-Gallego, Agustin Etxeberria, Haritz Sardon. CHEMICAL SCIENCE. Num. 32. Vol. 16. pp. 14509-14517. 2025. Científic.

• The need to implement FAIR principles in biomolecular simulations

  Rommie E. Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C. Biggin, Massimiliano Bonomi, Gregory R. Bowman, Richard A. Bryce, Giovanni Bussi, Paolo Carloni, David A. Case, Andrea Cavalli, Chia-En A. Chang, Thomas Cheatham, Margaret Cheung, Christophe Chipot, Lillian T. Chong, Preeti Choudhary, ...... ......, Vicente Moliner Ibáñez, ...... ......, Katarzyna Patrycja Swiderek, ....... ......, Modesto Orozco. NATURE METHODS . Vol. 22. pp. 641-645. 2025. Científic.

• A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

  Lorenzo Casalino, Carlos A. Ramos-Guzmán, Rommie E. Amaro, Carlos Simmerling, Alessio Lodola, Adrian J. Mulholland, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. JOURNAL OF PHYSICAL CHEMISTRY LETTERS. Num. 13. Vol. 16. pp. 3249-3263. 2025. Científic.

• Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age

  Katarzyna Patrycja Swiderek, Joan Bertran, Kirill Zinovjev, Iñaki Tuñón, Vicente Moliner Ibáñez. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. Num. 1. Vol. 15. pp. 1-18. 2025. Científic.

• Discovery of ICOS-Targeted Small Molecules Using Affinity Selection Mass Spectrometry Screening

  Longfei Zhang, Laura Calvo Barreiro, Víctor de Sousa Batista, Katarzyna Patrycja Swiderek, Moustafa T. Gabr. CHEMMEDCHEM. Num. 22. Vol. 19. pp. 1-8. 2024. Científic.

• Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

  Silvia Ferrer Castillo, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. ACS CATALYSIS. Num. 20. Vol. 14. pp. 15237-15249. 2024. Científic.

• A Single Amino Acid Able to Promote High-Temperature Ring-Opening Polymerization by Dual Activation

  Elena Gabirondo, Katarzyna Patrycja Swiderek, Edurne Marin, Ainhoa Maiz-Iginitz, Aitor Larranaga, Vicente Moliner Ibáñez, Agustin Etxeberria, Haritz Sardon. ADVANCED SCIENCE. Num. 16. Vol. 11. pp. 1-10. 2024. Científic.

• Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion

  Thomas L. Williams,, Irshad M. Taily, Lewis Hatton, Andrey A. Berezin, Yi-Lin Wu, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek, Yu-Hsuan Tsai, Louis Y. P. Luk. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. Num. 22. Vol. 63. pp. 1-12. 2024. Científic.

• Computational study of the mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis

  Katarzyna Patrycja Swiderek, Sergio Martí Forés, Kemel Arafet Cruz, Vicente Moliner Ibáñez. FARADAY DISCUSSIONS. Vol. 252. pp. 323-340. 2024. Científic.

• Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

  J. Javier Ruiz-Pernia, Katarzyna Patrycja Swiderek, Joan Bertran, Vicente Moliner Ibáñez, Inaki Tunon. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. Num. 5. Vol. 20. pp. 1783-1795. 2024. Científic.

• Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2

  Francisco J. Medrano, Sergio De la Hoz Rodríguez, Sergio Martí Forés, Kemel Arafet Cruz, Tanja Schirmeister, Stefan J. Hammerschmidt, Christin Mueller, Agueda Gonzalez-Martinez, Elena Santillana, John Ziebuhr, Antonio Romero, Collin Zimmer, Annabelle Weldert, Robert Zimmermann, Alessio Lodola, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Florenci Vicent González Adelantado. Communications Chemistry. Num. 1. Vol. 7. pp. 1-16. 2024. Científic.

• Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L

  Adrián Fernández de la Pradilla Ibáñez, Santiago Royo, Tanja Schirmeister, Fabian Barthels, Katarzyna Patrycja Swiderek, Florenci Vicent González Adelantado, Vicente Moliner Ibáñez. ACS CATALYSIS. Num. 20. Vol. 13. pp. 13354-13368. 2023. Científic.

• First-in-class small molecule inhibitors of ICOS/ICOSL interaction as a novel class of immunomodulators

  Somaya A. Abdel-Rahman, Katarzyna Patrycja Swiderek, Moustafa T. Gabr. RSC Medicinal Chemistry. Num. 9. Vol. 14. pp. 1767-1777. 2023. Científic.

• Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules

  Katarzyna Patrycja Swiderek, Susana Velasco-Lozano, Miquel Àngel Galmés Ordinas, Ion Olazabal, Haritz Sardon, Fernando Lopez-Gallego, Vicente Moliner Ibáñez. NATURE COMMUNICATIONS. Num. 1. Vol. 14. pp. 1-10. 2023. Científic.

• Unlocking a (Pseudo)-Mechanically Interlocked Molecule with a Coronene "Shoehorn"

  Susana Ibáñez Maella, Katarzyna Patrycja Swiderek, Eduardo Víctor Peris Fajarnés. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. Num. 18. Vol. 62. pp. 1-8. 2023. Científic.

• Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids

  Patricia Gomez de Santos,, Alejandro Gonzalez-Benjumea, Angela Fernandez-Garcia, Carmen Aranda, Yinqi Wu, Andrada But, Patricia Molina-Espeja, Diana M. Mate, David Gonzalez-Perez, Wuyuan Zhang, Jan Kiebist, Katrin Scheibner, Martin Hofrichter, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Julia Sanz-Aparici, Frank Hollmann, Miguel Alcalde, Ana Gutierrez. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. Num. 9. Vol. 62. pp. 1-9. 2023. Científic.

• Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States?

  Oluwafemi Akintola, Marco Farren-Dai, Weiwu Ren, Sandeep Bhosale, Robert Britton, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Andrew J. Bennet. ACS CATALYSIS. Num. 12. Vol. 23. pp. 14667-14678. 2022. Científic.

• Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases

  Miquel Àngel Galmés Ordinas, Alexander R. Nodling, Kaining He, Louis Y. P. Luk, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. CHEMICAL SCIENCE. Num. 7. Vol. 13. pp. 4779-4787. 2022. Científic.

• Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies

  Natalia Serrano Aparicio, Silvia Ferrer Castillo, Katarzyna Patrycja Swiderek. Pharmaceuticals. Num. 5. Vol. 15. pp. 1-21. 2022. Científic.

• Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

  Sergio Martí Forés, Kemel Arafet Cruz, Alessio Lodola, Adrian J. Mulholland, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. ACS CATALYSIS. Num. 1. Vol. 12. pp. 698-708. 2022. Científic.

• The role of streptavidin and its variants in catalysis by biotinylated secondary amines

  Alexander Nodling, Nicolo Santi, Raquel Castillo Solsona, Magdalena Lipka-Lloyd, Louis C. Morrill, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Louis Y. P. Luk. ORGANIC & BIOMOLECULAR CHEMISTRY . Num. 47. Vol. 19. pp. 10424-10431. 2021. Científic.

• Discovery of SARS-CoV-2 M-pro peptide inhibitors from modelling substrate and ligand binding

  Henry H. T. Chan, Marc A. Moesser, Rebecca K. Walters, Tika R. Malla, Rebecca M. Twidale, Tobias John, Helen M. Deeks, Tristan Johnston-Wood, Victor Mikhailov, Richard B. Sessions, William Dawson, Eidarus Salah, Petra Lukacik, Claire Strain-Damerell, C. David Owen, Takahito Nakajima, Katarzyna Patrycja Swiderek, Alessio Lodola, Vicente Moliner Ibáñez, David R. Glowacki, James Spencer, Martin A. Walsh, Christopher J. Schofield, Luigi Genovese, Deborah K. Shoemark, Adrian J. Mulholland, Fernanda Duarte, Garrett M. Morris. CHEMICAL SCIENCE. Num. 41. Vol. 12. pp. 13686-13703. 2021. Científic.

• On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome

  Natalia Serrano Aparicio, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. ACS CATALYSIS. Num. 18. Vol. 11. pp. 11806-11819. 2021. Científic.

• Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism

  Natalia Serrano Aparicio, Katarzyna Patrycja Swiderek, Iñaki Tuñón, Vicente Moliner Ibáñez, Joan Bertran. TOPICS IN CATALYSIS . Num. 1-4. Vol. 65. pp. 505-516. 2022. Científic.

• Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates-Glycopyranosyl Fluorides

  Marco Farren-Dai, Natalia Sannikova, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Andrew J. Bennet. ACS CATALYSIS. Num. 16. Vol. 11. pp. 10383-10393. 2021. Científic.

• Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides

  Miquel Àngel Galmés Ordinas, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. JOURNAL OF CHEMICAL INFORMATION AND MODELING. Num. 7. Vol. 61. pp. 3604-3614. 2021. Científic.

• Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes

  Miquel Àngel Galmés Ordinas, Alexander R. Nodling, Louis Luk, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. ACS CATALYSIS. Num. 14. Vol. 11. pp. 8635-8644. 2021. Científic.

• Enzymatic Delta(1)-Dehydrogenation of 3-Ketosteroids-Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism

  Michal Glanowski, Patrycja Wojcik, Magdalena Procner, Tomasz Borowski, Dawid Lupa, Przemyslaw Mielczarek, Maria Oszajca, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Andrzej J. Bojarski. ACS CATALYSIS. Num. 13. Vol. 11. pp. 8211-8225. 2021. Científic.

• Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog

  Svetlana A. Kholodar, Janet S. Finer-Moore, Katarzyna Patrycja Swiderek, Kemel Arafet Cruz, Vicente Moliner Ibáñez, Robert M. Stroud, Amnon Kohen. BIOCHEMISTRY. Num. 16. Vol. 60. pp. 1243-1247. 2021. Científic.

• Nature of Irreversible Inhibition of Human 20S Proteasome by Salinosporamide A. The Critical Role of Lys-Asp Dyad Revealed from Electrostatic Effects Analysis

  Natalia Serrano Aparicio, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. ACS CATALYSIS. Num. 6. Vol. 11. pp. 3575-3589. 2021. Científic.

• Transfer hydrogenations catalyzed by streptavidin-hosted secondary amine organocatalysts

  Nicolo Santi, Louis C. Morrill, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Louis Y. P. Luk. CHEMICAL COMMUNICATIONS . Num. 15. Vol. 57. pp. 1919-1922. 2021. Científic.

• Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity

  Kemel Arafet Cruz, Natalia Serrano Aparicio, Alessio Lodola, Adrian J. Mulholland, Florenci Vicent González Adelantado, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. CHEMICAL SCIENCE. Num. 4. Vol. 12. pp. 1433-1444. 2021. Científic.

• Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 M-pro by QM/MM computational methods

  Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. CHEMICAL SCIENCE. Num. 39. Vol. 11. pp. 10626-10630. 2020. Científic.

• Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design

  Weiwu Ren, Marco Farren-Dai, Natalia Sannikova, Katarzyna Patrycja Swiderek, Yang Wang, Oluwafemi Akintola, Robert Britton, Vicente Moliner Ibáñez, Andrew J. Bennet. CHEMICAL SCIENCE. Num. 38. Vol. 11. pp. 10488-10496. 2020. Científic.

• Discovery of a Histidine-Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine-Lyase

  Moustafa Gabr, Katarzyna Patrycja Swiderek. CHEMMEDCHEM. Num. 23. Vol. 15. pp. 2273-2279. 2020. Científic.

• Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis

  Aduragbemi S. Adesina, Katarzyna Patrycja Swiderek, Louis Y. P. Luk, Vicente Moliner Ibáñez, Rudolf K. Allemann. ACS CATALYSIS. Num. 14. Vol. 10. pp. 7907-7914. 2020. Científic.

• Exploring the Origin of Amidase Substrate Promiscuity in CALB by a Computational Approach

  Miquel Àngel Galmés Ordinas, Eduardo Garcia Junceda, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. ACS CATALYSIS. Num. 3. Vol. 10. pp. 1938-1946. 2020. Científic.

• Influence of Dielectric Environment upon Isotope Effects on Glycoside Heterolysis: Computational Evaluation and Atomic Hessian Analysis

  Katarzyna Patrycja Swiderek, Alexander J. Porter, Catherine M. Upfold, Ian H. Williams. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY . Num. 3. Vol. 142. pp. 1556-1563. 2020. Científic.

• Examination of the performance of semiempirical methods in QM/MM studies of the S(N)2-like reaction of an adenylyl group transfer catalysed by ANT4 '

  Sergio Martí Forés, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. THEORETICAL CHEMISTRY ACCOUNTS . Num. 11. Vol. 138. 2019. Científic.

• Molecular Insights into the Substrate-Assisted Mechanism of Viral DNA 3′-End Processing in Intasome of Prototype Foamy Virus Integrase from Molecular Dynamic and QM/MM Studies

  Agnieszka Krzeminska, Katarzyna Patrycja Swiderek. JOURNAL OF CHEMICAL INFORMATION AND MODELING. Num. 6. Vol. 59. pp. 2995-3005. 2019. Científic.

• A Molecular Modeling Approach to Identify Novel Inhibitors of the Major Facilitator Superfamily of Efflux Pump Transporters

  Sandra G. Zarate, Paula Morales, Katarzyna Patrycja Swiderek, Victor M. Bolanos Garcia, Agatha Bastida. ANTIBIOTICS. Num. 1. Vol. 8. 2019. Científic.

• Theoretical study of the inhibition mechanism of human 20S proteasome by dihydroeponemycin

  Natalia Serrano Aparicio, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY. Vol. 164. pp. 399-407. 2019. Científic.

• Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4 '-O-Nucleatidyltransferase

  Sergio Martí Forés, Agatha Bastida, Katarzyna Patrycja Swiderek. Frontiers in Chemistry. Vol. 6. pp. 1-11. 2019. Científic.

• Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease

  Kemel Arafet Cruz, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. ACS OMEGA. Num. 12. Vol. 3. pp. 18613-18622. 2018. Científic.

• Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase

  Ilya Gurevic, Zahidul Islam, Katarzyna Patrycja Swiderek, kai Trepka, Ananda K. Ghosh, Vicente Moliner Ibáñez, Amnon Kohen. ACS CATALYSIS. Num. 11. Vol. 8. pp. 10241-10253. 2018. Científic.

• Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools

  S.A. Kholodar, A.K. Ghosha, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, A. Kohen. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. Num. 41. Vol. 115. pp. 10311-10314. 2018. Científic.

• Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host

  Alexander R. Nödling, Katarzyna Patrycja Swiderek, Raquel Castillo Solsona, Jonathan W. Hall, Antonio Angelastro, Louis C. Morrill, Yi Jin, Yu-Hsuan Tsai, Vicente Moliner Ibáñez, Louis Y.P. Luk. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. Num. 38. Vol. 57. pp. 12478-12482. 2018. Científic.

• Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

  Weiwu Ren, Robert Pengelly, Marco Farren Dai, Saeideh Shamsi Kazem Abadi, Verena Oehler, Oluwafemi Akintola, Jason Draper, Michael Meanwell, Saswati Chakladar, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Robert Britton, Tracey M. Gloster, Andrew J. Bennet. NATURE COMMUNICATIONS. Vol. 9. 2018. Científic.

• Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling

  Katarzyna Patrycja Swiderek, Iñaki Tuñón, Ian H. Williams, Vicente Moliner Ibáñez. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY . Num. 12. Vol. 140. pp. 4327-4334. 2018. Científic.

• Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects

  Katarzyna Patrycja Swiderek, Alexander R. Nodling, Yu-Hsuan Tsai, Louis Y.P. Luk, Vicente Moliner Ibáñez. JOURNAL OF PHYSICAL CHEMISTRY A . Num. 1. Vol. 122. pp. 451-459. 2018. Científic.

• Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3

  Katarzyna Patrycja Swiderek, Iñaki Tuñón, Vicente Moliner Ibáñez, Joan Bertran. CHEMISTRY-A EUROPEAN JOURNAL. Num. 31. Vol. 23. pp. 7582-7589. 2017. Científic.

• Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations

  Erica Cristina Moreno Nascimento, Mónica Oliva Domínguez, Katarzyna Patrycja Swiderek, Joao B.L. Martins, Juan Manuel Andrés Bort. JOURNAL OF CHEMICAL INFORMATION AND MODELING. Num. 4. Vol. 57. pp. 958-976. 2017. Científic.

• Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme

  Katarzyna Patrycja Swiderek, Sergio Martí Forés, Iñaki Tuñón, Vicente Moliner Ibáñez, Juan Bertran. THEORETICAL CHEMISTRY ACCOUNTS . Num. 3. Vol. 136. 2017. Científic.

• Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer

  Katarzyna Patrycja Swiderek, Kemel Arafet Cruz, Amnon Koen, Vicente Moliner Ibáñez. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. Num. 3. Vol. 13. pp. 1375-1388. 2017. Científic.

• Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV‑1 Protease

  Agnieszka Krzeminska, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY . Num. 50. Vol. 138. pp. 16283-16298. 2016. Científic.

• Catalytic Enantioselective Epoxidation of Nitroalkenes

  Andreu Vidal Albalat, Katarzyna Patrycja Swiderek, Javier Izquierdo Ferrer, Santiago Rodríguez Pastor, Vicente Moliner Ibáñez, Florenci Vicent González Adelantado. CHEMINFORM. Num. 50. Vol. 47. 2016. Científic.

• Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 Variant

  J. Aranda, K. Zinovjev, Katarzyna Patrycja Swiderek, María Teresa Roca Moliner, I. Tuñón. ACS CATALYSIS. Num. 5. Vol. 6 . pp. 3262-3276. 2016. Científic.

• Catalytic enantioselective epoxidation of nitroalkenes

  Andreu Vidal Albalat, Katarzyna Patrycja Swiderek, Javier Izquierdo Ferrer, Santiago Rodríguez Pastor, Vicente Moliner Ibáñez, Florenci Vicent González Adelantado. CHEMICAL COMMUNICATIONS . Num. 52. Vol. 65 . pp. 1060-10063. 2016. Científic.

• Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesing New Diels-Alderases

  Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. JOURNAL OF PHYSICAL CHEMISTRY B . Num. 120. Vol. 8 . 2016. Científic.

• Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase

  A. Krzeminska, Katarzyna Patrycja Swiderek, P. Paneth. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. Num. 1. Vol. 18. pp. 310-317. 2016. Científic.

• Computational strategies for the design of new enzymatic functions

  Katarzyna Patrycja Swiderek, I. Tuñón, Vicente Moliner Ibáñez, J. Bertran. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. Vol. 582 . pp. 68-79. 2015. Científic.

• Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT

  A Krzeminska, P Paneth, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. JOURNAL OF PHYSICAL CHEMISTRY B . Num. 3. Vol. 119 . pp. 917-927. 2015. Científic.

• Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases?

  Isabel Bordes Pastor, J. Recatala, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. MOLECULES. Num. 10. Vol. 20 . pp. 17789-17806. 2015. Científic.

• Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17

  Katarzyna Patrycja Swiderek, I. Tuñón, Vicente Moliner Ibáñez, J. Beltran. ACS CATALYSIS. Num. 4. Vol. 5 . pp. 2587-2595. 2015. Científic.

• The Influence of Active Site Conformations on the Hydride Transfer step of the Thymidylate Synthase Reaction Mechanism

  Katarzyna Patrycja Swiderek, A. Kohen, Vicente Moliner Ibáñez. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. Num. 46. Vol. 17 . pp. 30793-30804. 2015. Científic.

• Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-SuccinyIbenzoate Synthase Using QM/MM Methods

  M. Sánchez-Tarín, Katarzyna Patrycja Swiderek, María Teresa Roca Moliner, I. Tuñón. JOURNAL OF PHYSICAL CHEMISTRY B . Num. 5. Vol. 119 . pp. 1899-1911. 2015. Científic.

• Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

  Katarzyna Patrycja Swiderek, I. Tuñon, Sergio Martí Forés, Vicente Moliner Ibáñez. ACS CATALYSIS. Num. 2. Vol. 5 . pp. 1172-1185. 2015. Científic.

• Peptide Bond Formation Mechanism Catalyzed by Ribosome

  Katarzyna Patrycja Swiderek, Sergio Martí Forés, I. Tuñón, Vicente Moliner Ibáñez, J. Bertran. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY . Num. 37. Vol. 137 . pp. 12024-12034. 2015. Científic.

• Theoretical Study of Primary Reaction of Pseudozyma antarctica Lipase B as the Starting Point To Understand Its Promiscuity

  Katarzyna Patrycja Swiderek, Sergio Martí Forés, Vicente Moliner Ibáñez. ACS CATALYSIS. Num. 2. Vol. 4 . pp. 426-434. 2014. Científic.

• Predicting enzymatic reactivity: from theory to desing

  Katarzyna Patrycja Swiderek, I Tuñón, Vicente Moliner Ibáñez. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE. Num. 5. Vol. 4 . pp. 407-421. 2014. Científic.

• Heavy enzymes - experimental and computational insights in enzyme dynamics )Review)

  Katarzyna Patrycja Swiderek, José Javier Ruiz Pernia, Vicente Moliner Ibáñez, I. Tuñón. CURRENT OPINION IN CHEMICAL BIOLOGY. Vol. 21 . pp. 11-18. 2014. Científic.

• Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects

  Katarzyna Patrycja Swiderek, Iñaki Tuñón, Sergio Martí Forés, Vicente Moliner Ibáñez, Juan Beltrán. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY . Num. 23. Vol. 135 . pp. 8708-8719. 2013. Científic.

• Do zwitterionic species exist in the non-enzymatic peptide bond formation?

  Katarzyna Patrycja Swiderek, Iñaki Tuñón, Sergio Martí Forés, Vicente Moliner Ibáñez, Juan Bertran. CHEMICAL COMMUNICATIONS . Num. 91. Vol. 48 . pp. 11253-11255. 2012. Científic.

• A theoretical study of carbon-carbon bond formation by a Michael-type addition

  Katarzyna Patrycja Swiderek, A. Pabis, Vicente Moliner Ibáñez. ORGANIC & BIOMOLECULAR CHEMISTRY . Num. 29. Vol. 10 . pp. 5598-5605. 2012. Científic.

• Theoretical studies of HIV-1 reverse transcriptase inhibition

  Katarzyna Patrycja Swiderek, Sergio Martí Forés, Vicente Moliner Ibáñez. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. Num. 36. Vol. 14 . pp. 12614-12624. 2012. Científic.

Capítols de llibre

• 32. GERMANIO (Ge)

  Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. La tabla periódica. (Espanya). Ed. Aranzadi; Aldana Gràfica AG. 2025. ISBN 9788419605115. Docent.

Aportacions a congressos

• QM/MM theoretical studies of enzyme catalyzed reactions

  Vicente Moliner Ibáñez, Sergio Martí Forés, Raquel Castillo Solsona, Katarzyna Patrycja Swiderek, María Teresa Roca Moliner, Kemel Arafet Cruz, Manuel Delgado, Daria De Raffele, Natalia Serrano Aparicio. 6th International Iberian Biophysics Congress X Iberoamerican Congress of Biophysics (2018 IIBC). Castelló (Espanya). 22-06-2018. Científic. 2018. ISSN 2445-4311.

Direcció de tesis

• Inhibition studies on the human 20S proteasome: molecular insights from a computational approach

  Autoria: Serrano Aparicio, Natalia. Institució: Universitat Jaume I (Espanya). Data lectura: 01/02/22. Direcció: Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek .

• Molecular insights into the promiscuity of serine hydrolases. Towards a computationally guided protocol for the redesign of enzymes

  Autoria: Galmés Ordinas, Miquel Àngel. Institució: Universitat Jaume I (Espanya). Data lectura: 20/01/22. Direcció: Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek .

• Theoretical studies of HIV-1 enzymes

  Autoria: Krzeminska Kowalska, Agnieszka. Institució: Lodz University of Technology (Polònia). Data lectura: 19-03-2019. Direcció: Swiderek, Katarzyna Patrycja.

Altres congressos

• Hands-on: Intro to QM/MM workflows

  Katarzyna Patrycja Swiderek. COMENZE Training School. Gerona (Espanya). 10-03-2026. Científic. 2026.

• Chemistry with computers

  Katarzyna Patrycja Swiderek. Workshop by the Computational Biochemistry research group, on the occasion of Science GTS 2025. Castellón (Espanya). 26-09-2025. Científic. 2025.

• Deciphering the role of protein electrostatic field in enzymatic catalysis: A case study of three distinct heterogeneous Proteasome β-subunits

  Katarzyna Patrycja Swiderek. CCPBioSim/CCP5 Multiscale Modelling Conference. Manchester (Regne Unit). 31-03-2025. Científic. 2025.

• Deciphering the role of protein electrostatic field in enzymatic catalysis: a case study of three distinct heterogeneous proteasome -subunits

  Katarzyna Patrycja Swiderek. IV Jornadas Españolas de Biocatálisis. San Sebastián (Espanya). 05-09-2024. Científic. 2024.

• Towards a New Protocol for Computer-Assisted Biocatalysts Design

  Katarzyna Patrycja Swiderek. 9th International Conference on Modeling Interaction in Biomolecules. Prague - Průhonice (Txeca, República). 10-09-2023. Científic. 2023.

• On the origin of the different reversible characters of inhibitors in the covalent inhibition of the human 20s proteasom

  Katarzyna Patrycja Swiderek. 9th Symposium on Theoretical Biophysics (TheoBio2023). Cetraro (Itàlia). 16-07-2023. Científic. 2023.

• QM/MM computational studies of the main protease of SARS-CoV-2: towards the design of new inhibitors

  Katarzyna Patrycja Swiderek. 4th International Caparica Christmas Conference on Translational Chemistry. IC3TC 2021. Capuchos, Caparica (Portugal). 08-12-2022. Científic. 2022.

• QM/MM studies on the covalent inhibition of human 20S proteasome

  Katarzyna Patrycja Swiderek. 16th Users Conference of the Spanish Supercomputing. Cáceres (Espanya). 14-09-2022. Científic. 2022.

• Qm/mm computational studies of the proteases: towards the design of new covalent inhibitors

  Katarzyna Patrycja Swiderek. 14th Girona Seminar. Gerona (Espanya). 31-05-2022. Científic. 2022.

• Towards a new protocol for computer assisted biocatalysts design

  Katarzyna Patrycja Swiderek. 10th International Symposium on Isotopomers (ISI) and 12th Isotopes Conference. Dübendorf (Suïssa). 29-05-2022. Científic. 2022.

• Computational studies on covalent inhibition of human 20S Proteasome as a complementary approach to the world of modern drug discovery

  Katarzyna Patrycja Swiderek. Emerging researchers in the Spanish Biocatalysis. (Online) (Espanya). 22-09-2021. Científic. 2021.

• Towards a new protocol for computer-assisted biocatalysts design

  Katarzyna Patrycja Swiderek. 43rd Annual Meeting of the Spanish Society of Biochemistry and Molecular Biology. (Online) (Espanya). 19-07-2021. Científic. 2021.

• QM/MM studies on the inhibition of human 20S proteasome; the role of electrostatic effects in biocatalysis

  Katarzyna Patrycja Swiderek. I Virtual GEQC-RSEQ Symposium. (Online) (Espanya). 17-06-2021. Científic. 2021.

• Towards a new protocol for computer assisted biocatalysts desing

  Katarzyna Patrycja Swiderek, A. Krzeminska, Miquel Àngel Galmés Ordinas, Vicente Moliner Ibáñez. CCPBioSim . Bristol (Regne Unit). 04-09-2019. Científic. 2019.

• Merging Theory and Experiments to Explore the Amidase Substrate Promiscuity in CALB

  Miquel Àngel Galmés Ordinas, Eduardo Garcia Junceda, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. 7th annual CCPBioSim Conference. Bristol (Regne Unit). 04-09-2019. Científic. 2019.

• Human 20S Proteasome inhibition: a computational approach

  Natalia Serrano Aparicio, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. 7 th annual CCPBioSim conference. Bristol (Regne Unit). 04-09-2019. Científic. 2019.

• Primary and Enzyme Kinetic Isotope Effects in E. Coli Thymidylate Synthase

  Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Amnon Koen. XIXth International Workshop on Quantum Atomic and Molecular Tunneling Systems. Sofia (Bulgària). 17-06-2019. Científic. 2019.

• Molecular Simulations of Iminium Organocatalysis anchored to Streptavidin

  A.R. Nodling, L.Y.P. Luk, Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez, Raquel Castillo Solsona. XXXVII Reunión Bienal de la Real Sociedad Española de Química (RSEQ). Donostia - San Sebastian (Espanya). 26-05-2019. Científic. 2019.

• Electrostatic. Dynamic or Compression Effects in Enzymatic Catalysis

  Katarzyna Patrycja Swiderek. The Future of Enzyme Modeling. University Stockholm (Suècia). 28-09-2018. Científic. 2018.

• Are electrostatic properties of proteins the origin of enzyme catalysis

  Katarzyna Patrycja Swiderek, A. Krzeminska, I. Tuñón, I. Williams, J. Bertrán, Vicente Moliner Ibáñez. 11th Congress on Electronic Structure: Principles and Applications. Toledo (Espanya). 17-07-2018. Científic. 2018.

• Dynamic and Electrostatic Effects in Enzymatic Catalysis. QM/MM Studies on HIV-1 Protease

  Katarzyna Patrycja Swiderek, Vicente Moliner Ibáñez. II Jornadas Españolas de BIOCATÁLISIS 2018. Oviedo (Espanya). 25-06-2018. Científic. 2018.

• Estudios teóricos sobre el origen de la eficiencia catalítica de las enzimas

  Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek, Iñaki Tuñón, Ian Williams, Joan Bertran. XLIIIème Congrès des Chimistes Théoriciens d'Expression Latine (QUITEL-CHITEL 2017). Paris (França). 03-07-2017. Científic. 2017.

• Catalytic enantioselective epoxidation of nitroalkenes

  Andreu Vidal Albalat, Katarzyna Patrycja Swiderek, Santiago Rodríguez Pastor, Vicente Moliner Ibáñez, Florenci Vicent González Adelantado. XXXVI Reunión bienal de la Real Sociedad ESpañola de Química. Sitges (Espanya). 25-06-2017. Científic. 2017.

• QM/MM Studies on HIV-1 Protease

  A. Krzeminska, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. Gordon Research Conferences. Girona (Espanya). 24-07-2016. Científic. 2016.

• QM/MM studies on HIV-1 protease

  A. Krzeminska, Vicente Moliner Ibáñez, Katarzyna Patrycja Swiderek. ESPA2016. Castelló (Espanya). 28-06-2016. Científic. 2016.

• Enzyme mechanisms by biological systems

  Katarzyna Patrycja Swiderek, Iñaki Tuñón, Vicente Moliner Ibáñez, Juan Bertran. EMBO Courses & Workshops. Manchester (Regne Unit). 01-06-2014. Científic. 2014.

• Reaction mechanism and molecular dynamics analysis of M. Hhai C5-Cytosine-methyltransferase

  J. Aranda, K. Zinovjev, Katarzyna Patrycja Swiderek, María Teresa Roca Moliner, I. Tuñón. 9th European Conference on Computational Chemistry EuCo-CC9. Sopron (Hongria). 01-09-2013. Científic. 2013.

• Molecular dynamics and QM/MM free energy profiles of cytosine C5-methyltransferase M. Hhai

  J Aranda, K. Zinovjev, Katarzyna Patrycja Swiderek, María Teresa Roca Moliner, I. Tuñón. 38th Federation of European Biochemical Societies Congress 2013 FEBS. St Petersburg (Rússia). 06-07-2013. Científic. 2013.

• Theoretical Study of the binding of some classical inhibitors to Acetylcholinesterase

  Erica Cristina Moreno Nascimento, Katarzyna Patrycja Swiderek, Mónica Oliva Domínguez, Juan Manuel Andrés Bort, B.L. Martins. 6th. Internacional Theoretical Biophysics Symposium (TheoBio 2013). Gothenburg, Sweden (Suècia). 24-06-2013. Científic. 2013.

• Lactase Dehydrogenase - Mistery of Catalysis

  Katarzyna Patrycja Swiderek, Sergio Martí Forés, Vicente Moliner Ibáñez. Isotopes 2013. Sopot (Polònia). 16-06-2013. Científic. 2013.

• Theoretical study of acetylchlinesterase inhibition (Pòsster)

  Erica Cristina Moreno Nascimento, Katarzyna Patrycja Swiderek, Mónica Oliva Domínguez, Juan Manuel Andrés Bort, J.B. Lopes Martins. XXXVIII Congress of Theoretical Chemists of Latin Expression (QUITEL 2012.). Natal (Brasil). 02-12-2012. Científic. 2012.

Conferències impartides

• Covalent Inhibitors of Proteases: Towards the Computer Assisted Design

  Katarzyna Patrycja Swiderek. Seminar Programme. CICbiomaGUNE (Espanya). 28-09-2023.

• Theoretical studies of reactivity in cellular processes

  Katarzyna Patrycja Swiderek. University Cardiff (Regne Unit). 25-04-2019.

• QM/MM studies of peptide bond formation

  Katarzyna Patrycja Swiderek. Computational Chemistry Research Seminar. University of Bath (Regne Unit). 30-06-2017.

Comité revistes científiques

• BIOCHEM. 2021. Comité editorial-Consell redacció. ISSN 2673-6411.