-2025-
84. L. Casalino, C. A. Ramos-Guzmán, R. E. Amaro*, C. Simmerling*, A. Lodola*, A. J. Mulholland*, K. Świderek*, V. Moliner* "A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats" J. Phys. Chem. Lett. 16, 3249–3263 (2025) DOI:10.1021/acs.jpclett.4c03654
83. R. Amaro, J. Åqvist, I. Bahar, F. Battistini, A. Bellaiche, D. Beltran, P. C. Biggin, M. Bonomi, G. R. Bowman, R. Bryce, G. Bussi, P. Carloni, D. Case, A. Cavalli, C.-E. A. Chang, T. E. C. III, M. S. Cheung, C. Chipot, L. T. Chong, P. Choudhary, G. A. Cisneros, C. Clementi, R. Collepardo-Guevara, P. Coveney, R. Covino, T. D. Crawford, M. D. Peraro, B. de Groot, L. Delemotte, M. D. Vivo, J. Essex, F. Fraternali, J. Gao, J. L. Gelpí, F. L. Gervasio, F. D. Gonzalez-Nilo, H. Grubmüller, M. Guenza, H. V. Guzman, S. Harris, T. Head-Gordon, R. Hernandez, A. Hospital, N. Huang, X. Huang, G. Hummer, J. Iglesias-Fernández, J. H. Jensen, S. Jha, W. Jiao, W. L. Jorgensen, S. C. L. Kamerlin, S. Khalid, C. Laughton, M. Levitt, V. Limongelli, E. Lindahl, K. Lindorff-Larsen, S. Loverde, M. Lundborg, Y. L. Luo, F. J. Luque, C. I. Lynch, A. MacKerell, A. Magistrato, S. J. Marrink, H. Martin, J. A. McCammon, K. Merz, V. Moliner, A. Mulholland, S. Murad, A. N. Naganathan, S. Nangia, F. Noe, A. Noy, J. Oláh, M. O’Mara, M. J. Ondrechen, J. N. Onuchic, A. Onufriev, S. Osuna, A. R. Panchenko, S. Pantano, C. Parish, M. Parrinello, A. Perez, T. Perez-Acle, J. R. Perilla, B. M. Pettitt, A. Pietropalo, J.-P. Piquemal, A. Poma, M. Praprotnik, M. J. Ramos, P. Ren, N. Reuter, A. Roitberg, E. Rosta, C. Rovira, B. Roux, U. Röthlisberger, K. Y. Sanbonmatsu, T. Schlick, A. K. Shaytan, C. Simmerling, J. C. Smith, Y. Sugita, K. Świderek, M. Taiji, P. Tao, I. G. Tikhonova, J. Tirado-Rives, I. Tunón, M. W. V. d. Kamp, D. V. der Spoel, S. Velankar, G. A. Voth, R. Wade, A. Warshel, V. V. Welborn, S. Wetmore, C. F. Wong, L.-W. Yang, M. Zacharias, M. Orozco. "The need to implement FAIR principles in biomolecular simulations." Nat Methods 22, 641–645 (2025). DOI:10.1038/s41592-025-02635-0
82. K. Świderek, J. Bertran, K. Zinovjev, I. Tuñón, V. Moliner "Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age" WIREs Computational Molecular Science 15, e70003 (2025) DOI:10.1002/wcms.70003
-2024-
81.S. Ferrer, V. Moliner, K. Świderek* "Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits" ACS Catal. 14, 15237 (2024) DOI:10.1021/acscatal.4c04964
80. L. Zhang, L. Calvo-Barreiro, V. de Sousa Batista, K. Świderek,* M. T. Gabr* "Discovery of ICOS-Targeted Small Molecules Using Affinity Selection Mass Spectrometry Screening" ChemMedChem. e202400545 (2024) DOI:10.1002/cmdc.202400545
79. L. Williams, I.M. Taily, L Hatton, A.A. Berezin, Y.L. Wu, V. Moliner, K. Świderek*, Y. Tsai*, L.Y.P Luk* "Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion" Angew. Chemie Int. Ed. e202403098 (2024) DOI:10.1002/ange.202403098
78. K. Świderek*, S. Marti, K. Arafet, V. Moliner* "Computational study of the Mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis" Faraday Discussions Accepted Manuscript (2024) DOI: 10.1039/D4FD00022F
77. J.J. Ruiz-Pernía, K. Świderek, J. Bertran, V. Moliner, I. Tuñón "Electrostatics as a Guiding Principle in Understanding and Designing Enzymes" J. Chem. Theory Comput. 20, 1783 (2024) DOI:10.1021/acs.jctc.3c01395
76. E. Gabirondo, K. Świderek, E. Marin, A. Maiz-Iginitz, A. Larranaga, V. Moliner, A. Etxeberria, H. Sardon "A Single Amino Acid Able to Promote High-Temperature Ring-Opening Polymerization by Dual Activation" Adv. Sci., 2308956 (2024) DOI: 10.1002/advs.202308956
75. F. J. Medrano, S. de la Hoz-Rodríguez, S. Martí, K. Arafet, T. Schirmeister, S. J. Hammerschmidt, C. Müller, Á. González-Martínez, E. Santillana, J. Ziebuhr, A. Romero, C. Zimmer, A. Weldert, R. Zimmermann, A. Lodola, K. Świderek, V. Moliner, F. V. González "Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2." Commun Chem 7, 15 (2024). DOI: 10.1038/s42004-024-01104-7
-2023-
74. A. Fernández-de-la-Pradilla, S. Royo, T. Schirmeister, F. Barthels, K. Świderek*, F. V. González*, V. Moliner* "Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L" ACS Catal. 13, 13354-13368 (2023) doi:10.1021/acscatal.3c02748
73. S.A. Abdel-Rahman, K. Świderek, M.T. Gabr "First-in-class small molecule inhibitors of ICOS/ICOSL interaction as a novel class of immunomodulators" RSC Med. Chem. 14, 1767-1777 (2023) doi:10.1039/D3MD00150D
72. K. Świderek*, S. Velasco-Lozano, M. À. Galmés, I. Olazabal, H. Sardon, F. López-Gallego*, V. Moliner* "Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules" Nat. Commun. 14:3556. (2023) doi:10.1038/s41467-023-39201-1
71. S. Ibáñez,§ K. Świderek,§ E. Peris "Unlocking a (pseudo)‐Mechanically Interlocked Molecule with a Coronene “Shoehorn“"
Angew. Chemie Int. Ed. Just accepted (2023) doi:10.1002/anie.202301914
§ - These authors have contributed equally
70. P. Gomez de Santos, A. González-Benjumea, A. Fernandez-Garcia, C. Aranda, Y. Wu, A. But, P. Molina-Espeja, D. Mate Maté, D. Gonzalez-Perez, W. Zhang, J. Kiebist, K. Scheibner, M. Hofrichter, K. Świderek, V. Moliner, J. Sanz-Aparicio, F. Hollmann, A. Gutiérrez, M. Alcalde "Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids" Angew. Chemie Int. Ed. e202217372 (2023) doi: 10.1002/anie.202217372
-2022-
69. O. Akintola, M. Farren-Dai, W. Ren, S. Bhosale, R. Britton, K. Świderek, V. Moliner, and A. J. Bennet "Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States?" ACS Catal. 12, 14667–14678 (2022). doi: 10.1021/acscatal.2c04027
68. N. Serrano-Aparicio, S. Ferrer, K. Świderek* "Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies" Pharmaceuticals 15, 531, (2022). doi:10.3390/ph15050531
67. M. À. Galmés, A. R. Nodling, K. He, L. Y. P. Luk*, K. Świderek*, V. Moliner* "Computational design of an amidase by combining
the best electrostatic features of two promiscuous hydrolases" Chem. Sci. just accepted (2022) doi:10.1039/d2sc00778a
66. S. Martí, K. Arafet, A. Lodola, A. J. Mulholland, K. Świderek*, V. Moliner* "Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations" ACS Catal. 12, 1, 698–708 (2022) doi: 10.1021/acscatal.1c04661
-2021-
65. A. R. Nödling, N. Santi, R. Castillo, M. Lipka-Lloyd, Y. Jin, L. C. Morrill, K. Świderek,* V. Moliner*, L. Y. P. Luk* "The role of streptavidin and its variants in catalysis by biotinylated secondary amines" Org. Biomol. Chem. 19, 10424-10431, (2021). doi:10.1039/D1OB01947C
64. N. Serrano-Aparicio, V.Moliner*, K. Świderek* "On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome" ACS Catal. 11, 11806–11819, (2021) doi:10.1021/acscatal.1c02614
63. H.T.H. Chan, M.A. Moesser, R.K. Walters, T.R. Malla, R.M. Twidale, T. John, H.M. Deeks, T. Johnston-Wood, V. Mikhailov, R.B. Sessions, W. Dawson, E. Saleh, P. Lukacik, C. Strain-Damerell, C.D. Owen, T. Nakajima, K. Świderek, A. Lodola, V. Moliner, D.R. Glowacki, J. Spencer, M.A.A. Walsh, C.J. Schofield, L. Genovese, D.K. Shoemark, A.J. Mulholland, F. Duarte, G.M. Morris "Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding" Chem. Sci. (2021) 12, 13686-13703 doi:10.1039/D1SC03628A
62. N. Serrano-Aparicio, K. Świderek*, I. Tuñón, V.Moliner*, J. Bertran "Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism" Top Catal 1-12 (2021) doi:10.1007/s11244-021-01494-1
61. M. Farren-Dai, N. Sannikova, K. Świderek*, V. Moliner*, A.J. Bennet* "Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates–Glycopyranosyl Fluorides" ACS Catal. 11, 10383-10393 (2021) doi:10.1021/acscatal.1c01918
60. M. À. Galmés,K. Świderek*, V. Moliner* "Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides" J. Chem. Inf. Model. 61, 3604–3614 (2021) doi:10.1021/acs.jcim.1c00425
59. M. À. Galmés, A. R. Nödling, L. Luk*, K. Świderek*, V. Moliner* "Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes" ACS Catal. 11, 8635–8644 (2021) doi:10.1021/acscatal.1c02150
58. M. Glanowski, P. Wójcik, M. Procner, T. Borowski, D. Lupa, P. Mielczarek, M. Oszajca, K. Świderek, V. Moliner, A. J. Bojarski, M. Szaleniec "Enzymatic Δ1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism" ACS Catal. 11, 8211–8225 (2021) doi: 10.1021/acscatal.1c01479
57. S. A. Kholodar, J. S. Finer-Moore, K. Świderek, K. Arafet, V. Moliner, R. M.Stroud, A. Kohen "Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog." Biochemistry 60, 1243-1247 (2021) doi: 10.1021/acs.biochem.1c00063
56. N. Serrano-Aparicio, V.Moliner*, K. Świderek* "Nature of Irreversible Inhibition of Human 20S Proteasome by Salinosporamide A. The Critical Role of Lys–Asp Dyad Revealed from Electrostatic Effects Analysis" ACS Catal. 11, 3575–3589, (2021) doi:10.1021/acscatal.0c05313
55. N. Santi, L. C. Morrill, K. Świderek, V. Moliner, L.Y.P. Luk "Transfer Hydrogenations catalyzed by Streptavidin-hosted Secondary Amine Organocatalyst" Chem. Commun. 57, 1919-1922 (2021) doi:10.1039/D0CC08142F
54. K. Arafet, N. Serrano-Aparicio A. Lodola A. Mulholland, F. V. González, K. Świderek*, V. Moliner* "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." Chem. Sci. 12, 1433-1444 (2021) doi:10.1039/D0SC06195F ChemRxiv Preprint Doi: 10.26434/chemrxiv.12941819.v1
-2020-
53. K. Świderek, J. J. Ruiz, I. Tuñón, V. Moliner. "Computational Insights Into Enzyme Catalysis." Comprehensive Natural Products III, Chemistry and Biology, Volume 4: Enzymes and Enzyme Mechanisms (Polar Intermediates). 4, pp. 560 - 577. Elsevier, (2020).
52. W. Ren, M. Farren-Dai, N. Sannikova, K. Świderek, Y. Wang, O. Akintola, R. Britton, V. Moliner, A. J Bennet "Glycoside Hydrolase Stabilization of Transition State Charge: New Directions for Inhibitor Design" Chem.Sci. 11, 10488-10495 (2020) doi:10.1039/D0SC04401F
51. M. Gabr*, K. Świderek* "Discovery of a histidine‐based scaffold as an inhibitor of gut microbial choline trimethylamine‐lyase." ChemMedChem 15, 2273-2279 (2020) doi:10.1002/cmdc.202000571
50. K. Świderek*, V. Moliner* "Revealing the Molecular Mechanisms of Proteolysis of SARS-CoV-2 Mpro from QM/MM Computational Methods." Chem. Sci. 11, 10626-10630 (2020) doi:10.1039/D0SC02823A ChemRxiv Preprint Doi: 10.26434/Chemrxiv.12283967.V1This Article Is Part Of The Themed Collection: 2020 Chemical Science HOT Article Collection And Celebrating 10 Years Of Chemical Science
49. A.S. Adesina,§ K. Świderek,§ L.Y.P. Luk, V. Moliner, R.K. Allemann "Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis" ACS Catal. 10, 7907-7914 (2020) doi:10.1021/acscatal.0c01856
§ - These authors have contributed equally
48. K. Świderek, A. Porter, C. M. Upfold, I. H. Williams "Influence of dielectric environment upon isotope effects on glycoside heterolysis: computational evaluation and atomic hessian analysis." J. Am. Chem. Soc. 142, 1556-1563 (2020) doi:10.1021/jacs.9b11988
47. M.A. Galmés, E. García-Junceda*, K. Świderek*, V. Moliner* "Exploring the Origin of Amidase Substrate Promiscuity in CALB by a Computational Approach." ACS Catal. 10, 1938-1946 (2020), ACS Editors' Choice doi:10.1021/acscatal.9b04002
-2019-
46. S. Martí, V. Moliner*, K. Świderek* "Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′" Theor Chem Acc 138:120 (2019) doi:10.1007/s00214-019-2507-1
45. A. Krzeminska, K. Świderek* "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." J. Chem. Inf. Model. 59, 2995-3005 (2019) doi:10.1021/acs.jcim.9b00276
44. S. G. Zárate, P. Morales, K. Świderek, V. M. Bolanos-Garcia, A. Bastida "A Molecular Modeling Approach to Identify Novel Inhibitors of the Major Facilitator Superfamily of Efflux Pump Transporters" Antibiotics 8, 25 (2019) doi:10.3390/antibiotics8010025
43. N. Serrano-Aparicio, K. Świderek*, V. Moliner* "Theoretical study of the inhibition mechanism of human 20S proteasome by dihydroeponemycin." Eur. J. Med. Chem. 164, 399-407 (2019) DOI: 10.1016/j.ejmech.2018.12.062
42. S. Marti, A. Bastida, K. Świderek* "Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4’-O-Nucleotidyltransferase."
Front. Chem. 6, 660 (2019) DOI: 10.3389/fchem.2018.00660
-2018-
41. K. Arafet, K. Świderek, V. Moliner "Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease." ACS Omega 3, 18613-18622 (2018) DOI: 10.1021/acsomega.8b03010
40. S.A. Kholodar, A. K. Ghosh, K. Świderek, V. Moliner, A. Kohen "Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools." Proc. Nat. Acad. Sci. USA. 115, 10311-10314 (2018) DOI: 10.1073/pnas.1811059115
39. I. Gurevic, Z. Islam, K. Świderek, K. Trepka, A. K Ghosh, V. Moliner, A. Kohen "Experimental and computational studies delineate the role for asparagine 177 in hydride transfer for E. coli thymidylate synthase." ACS Catal. 8, 10241-10253 (2018) DOI: 10.1021/acscatal.8b02554
38. W. Ren, R. Pengelly, M. Farren-Dai, S. Shamsi Kazem Abadi, V. Oehler, O. Akintola, J. Draper, M. Meanwell, S. Chakladar, K. Świderek, V. Moliner, R. Britton, T. M. Gloster, A. J. Bennet "Revealing the mechanism for covalent inhibition ofglycoside hydrolases by carbasugars at an atomiclevel" Nat. Commun. 9: 3243 (2018) DOI: 10.1038/s41467-018-05702-7
37. A.R. Nödling, K. Świderek, R. Castillo, J.W.Hall, A. Angelastro, L.C. Morrill, Y. Jin, Y. Tsai, V. Moliner, L.Y.P. Luk "Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host" Angew. Chem. Int. Ed. 57, 12478-12482 (2018) F1000Prime Highlights DOI: 10.1002/anie.201806850
36. K. Świderek, I. Tuñón, I. H. Williams,V. Moliner "Insights on the origin of catalysis on glycine N-methyltransferase from computational modelling" J. Am. Chem. Soc. 140, 4327–4334, (2018) JACS Highlights, Biofisica Highlights, F1000Prime Highlights DOI: 10.1021/jacs.7b13655
35. K. Świderek, A. R. Nödling, Y. Tsai, L. Y. P. Luk, V. Moliner "The Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effect" J. Phys. Chem. A, 122, 451–459, (2018) DOI: 10.1021/acs.jpca.7b11803
-2017-
34. K. Świderek, I. Tuñón, V. Moliner, J. Bertran "Revealing the origin of the efficiency of the de novo designed Kemp eliminase HG-3.17 by comparison with the former developed HG-3" Chem. Eur. J. 23, 7582–7589, (2017) DOI: 10.1002/chem.201700807
33. K. Świderek, S. Marti, I. Tuñón, V. Moliner, J. Bertran "Molecular mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a twister ribozyme" Theor Chem Acc 136:31, (2017) DOI: 10.1007/s00214-017-2060-8
32. K. Świderek, K. Arafet, A. Kohen, V. Moliner "Benchmarking QM/MM Methods on the Thymidylate Synthase Catalyzed Hydride Transfer." J. Chem. Theory Comput. 13, 1375–1388, (2017) DOI: 10.1021/acs.jctc.6b01032
31. É. C. M. Nascimento, M. Oliva, K. Świderek, J. B. L. Martins, J. Andrés "Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations"
J. Chem. Inf. Model. 57, 958-976 (2017) DOI: 10.1021/acs.jcim.7b0003
-2016-
30. A. Krzemińska, V. Moliner*, K. Świderek* "Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease."
J. Am. Chem. Soc. 138, 16283–16298 (2016) DOI: 10.1021/jacs.6b06856
29. A. Vidal-Albalat, K. Świderek, J. Izquierdo, S. Rodriguez, V. Moliner and F. V. Gonzalez "Catalytic Enantioselective Epoxidation of Nitroalkenes" Chem Commun. 52, 10060-10063 (2016) DOI: 10.1039/C6CC03539F
28. K. Świderek and V. Moliner "Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesign New Diels-Alderases" J. Phys. Chem. B 120, 2053-2070 (2016) DOI: 10.1021/acs.jpcb.5b10527
27. J. Aranda, K. Zinovjev, K. Świderek, M. Roca, I.Tuñón "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." ACS Catal. 6, 3262 - 3276 (2016)
doi: 10.1021/acscatal.6b00394
-2015-
26. A. Krzeminska, K. Świderek, P. Paneth "Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase." Phys. Chem. Chem. Phys. 18, 310-317, (2015) DOI: 10.1039/c5cp06050h
25. I. Bordes, J. Recatá, K. Świderek*, V. Moliner* "Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases"
Molecules 20,17789-17806 (2015) DOI: 10.3390/molecules201017789
24. K. Świderek, S. Martí, I. Tuñon, V. Moliner, J. Bertran, "Peptide Bond Formation Mechanism Catalyzed by Ribosome."
J. Am. Chem. Soc. 137, 12024-12034 (2015) DOI: 10.1021/jacs.5b05916
23. K. Świderek, A. Kohen, V. Moliner "Influence of Active Site Conformations on the Hydride Transfer step of the Thymidylate Synthase Reaction Mechanism" Phys. Chem. Chem. Phys. 17, 30793-30804 (2015) DOI: 10.1039/C5CP01239B
22. K. Świderek, I. Tuñón, V. Moliner, J. Bertran "Computational strategies for the design of new enzymatic functions."
Arch. Biochem. Biophys., 582, 68–79 (2015) DOI: 10.1016/j.abb.2015.03.013
21. K. Świderek, I. Tuñón, V. Moliner, J. Bertran "Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalysed by HG3.17" ACS Catalysis 5, 2587-2595, (2015) DOI: 10.1021/cs501904w
20. K. Świderek*, I. Tuñón, S. Martí, V. Moliner* "Protein Conformational Landscapes and Catalysis. Influence of active site conformations in the reaction catalyzed by L-Lactate Dehydrogenase." ACS Catal., 5, 1172-1185, (2015) DOI: 10.1021/cs501704f
19. M. Sanchez Tarin, K. Świderek, M. Roca, I. Tuñón. "Enzyme Promiscuity in Enolase Superfamily. A Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods." J. Phys. Chem. B. 119, 1899 - 1911 (2015) DOI: 10.1021/jp511147b
18. A. Krzeminska, P. Paneth, V.Moliner*, K. Świderek* "Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT" J. Phys. Chem. B 119, 917-927, (2015) DOI: 10.1021/jp506119h
-Before 2015-
17. K. Świderek, J. J. Ruiz Pernia, V. Moliner; I. Tuñón "Heavy enzymes — experimental and
computational insights in enzyme dynamics."
Curr. Opinion Chem.Biol. 21, 11 - 18 (2014)
16. K. Świderek, I. Tuñon, V. Moliner "Predicting enzymatic reactivity:from theory to design." WIREs Comput Mol Sci 4, 407-421 (2013)
14. K. Świderek, S. Martí, V. Moliner "Theoretical study of primary reaction of Pseudozyma antarctica lipase B as the starting point to understand its promiscuity. ACS Catal. 4,426 - 434 (2013).
13. K. Świderek, I. Tuñon, S. Martí, V.Moliner J. Bertrán "Role of solvent on non-enzymatic
peptide bond formation mechanisms and Kinetic Isotope Effects." J. Am. Chem. Soc. 135, 8708 - 8719 (2013).
12. K. Świderek, I. Tuñon, S. Martí, V. Moliner, J. Bertrán. "Do zwitterionic species exist in the
non-enzymatic peptide bond formation?"
Chem. Commun. 48, 11253 - 11255 (2012).
11. K. Świderek, S. Martí, V. Moliner "Theoretical Studies of HIV-1 reverse transcriptase inhibition."
Phys. Chem. Chem. Phys. 14, 12614 - 12624. (2012).
10. K. Świderek, A. Pabis, V. Moliner "A Theoretical Study of Carbon-Carbon Bond Formation by a
Michael-Type Addition."
Org. Biomol.Chem. 10, 5598 - 5605 (2012)
9. K. Świderek, P.Paneth "Extending Limits of Chlorine Kinetic Isotope Effects." J. Org. Chem. 77, 5120 - 5124 (2012).
8. A. Siwek, K. Świderek, S. Jankowski "Problems with molecular mechanics implementations on the
example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide." J. Mol. Model. 18, 843 - 849 (2011).
7. K Świderek*, P. Paneth "Binding Ligands and Cofactor to L-Lactate Dehydrogenase from Human
Skeletal and Heart Muscles.
J. Phys. Chem. B 115, 6366 - 6376 (2011)
6. K. Świderek, P. Paneth "Differences and similarities in binding of pyruvate and L-lactate in the active site
of M4 and H4 isoforms of human lactate dehydrogenase from binding isotope effects" Arch. Biochem. Biophys. 506, 33 - 41 (2011)
5. K. Świderek, A. Dybala Defratyka, D. Rohr. "A new scheme to calculate isotope effects." J. Mol. Model. 17, 2175 - 2182 (2010)
4. K. Świderek, P. Paneth "Importance of the Lactate Dehydrogenase Quaternary Structure in Theoretical
Calculations." J. Phys. Chem. B 114, 3393 - 3397 (2010)
3. K. Świderek, A. Panczakiewicz, A. Bujacz, G. Bujacz, P. Paneth "Modeling of Isotope
Effects on Binding Oxamate to Lactic Dehydrogenase."
J. Phys. Chem. B 113, 12782 -
12789 (2009).
2.K. Świderek, P. Paneth "Modeling excitation properties of iridium complexes." J. Phys.
Org. Chem. 22, 845 - 856. (2009).
1. J. Dzierzawska, A. Jarota; M. Karolak, L. Piotrowski, I. Placek, K. Świderek, L. Szatkowski, P. Paneth "Carbon and secondary deuterium kinetic isotope effects on SN2 methyl transfer
reactions." J. Phys.
Org. Chem. 20, 1114 - 1120 (2007)
Cover of Issue 13, 2025
J. Phys. Chem. Lett., 2025, 16, 3185-3401
Cover of Issue 6, 2021
ACS Catal., 2021, 11, 3575–3589
Front Cover of Issue 39, 2020
Chem. Sci., 2020, 11, 10626-10630
Cover of Issue 3, 2020
ACS Catal., 2020, 10, 1938-1946
Cover of Issue 12, 2018
J. Am. Chem. Soc. 2018 140, 4327–4334
Cover of Issue 46, 2015
PCCP, 2015, 17, 30793-30804
LDH Structure (PDB: 3H3F)
J. Phys. Chem. B 113, 12782 - 12789 (2009)