Citations – AQUA-DUCT by Tunneling Group.

AQUA-DUCT citations:

2025

ESTEEM Strategy: Revolutionizing Enzymatic Catalysis through the Evolutionary Gateway of Enzyme Tunnels R. Dong, J. Wang, J. Tian, G. Xu, Z. Liang, X. Qin, X. Wang, X. Liu, H. Luo, B. Yao, Y. Wang, T. Tu, ACS Catal., vol. 15, no. 23, pp. 20108–20122, 2025, Nov 21, DOI: https://doi.org/10.1021/acscatal.5c03170 ARTICLE

WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families A.-L. R. Brownless, T. Harrison-Rawn, S. C. L. Kamerlin, JACS Au, vol. 5, no. 12, pp. 6379–6395, 2025 Nov 20, DOI: https://doi.org/10.1021/jacsau.5c00447 ARTICLE

Capturing intrinsic protein dynamics for explaining beneficial substitutions from protein engineering campaigns S. Meng, Z. Li, P. Zhang, Y. Ji, U. Schwaneberg, Biotechnology Advances, vol. 83, p. 108660, 2025, Oct, DOI: https://doi.org/10.1016/j.biotechadv.2025.108660 ARTICLE

Interfacial Anchoring of Haloalkane Dehalogenase LinB for Efficient 1‐Bromobutane Degradation S. Zhang, Y. Han, M. Sun, K. Zhu, H. Zhou, L. Wang, G. Jiang, D. Lu, Z. Liu, ChemCatChem, vol. 17, no. 17, 2025, Jul 3, DOI: https://doi.org/10.1002/cctc.202500812 ARTICLE

Effect of Trimethylamine‐N‐Oxide (TMAO) and Sorbitol on the Catalytic Activity of Candida boidinii Formate Dehydrogenase J.A. Perez‐Erviti, Y. Almeida-Hernandez, J. Mieres-Perez, N. Gajardo-Parra, R. Winter, C. Held, G. Sadowski, E. Sanchez-Garcia, ChemCatChem, vol. 17, no. 11, 2025, Apr 28, DOI: https://doi.org/10.1002/cctc.202401961 ARTICLE

Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age K. Świderek, J. Bertran, K. Zinovjev, I. Tuñón, V. Moliner, WIREs Comput Mol Sci, vol. 15, no. 1, 2025, Jan 19, DOI: https://doi.org/10.1002/wcms.70003 ARTICLE

PathInHydro, a Set of Machine Learning Models to Identify Unbinding Pathways of Gas Molecules in [NiFe] Hydrogenases F. Sohraby, J.-Y. Guo, A. Nunes-Alves, J. Chem. Inf. Model., vol. 65, no. 2, pp. 589–602, 2025, Jan 7, DOI: https://doi.org/10.1021/acs.jcim.4c01656 ARTICLE

2024

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model A. S. Thirunavukarasu, K. Szleper, G. Tanriver, I. Marchlewski, K. Mitusińska, A. Góra, J. Brezovsky, J. Chem. Inf. Model., vol. 65, no. 1, pp. 326–337, 2024, Dec 16, DOI: https://doi.org/10.1021/acs.jcim.4c01177 ARTICLE

Impact of water models on the structure and dynamics of enzyme tunnels A. Sethi, N. Agrawal, J. Brezovsky, Computational and Structural Biotechnology Journal, vol. 23, pp. 3946–3954, 2024, Nov 2, DOI: https://doi.org/10.1016/j.csbj.2024.10.051 ARTICLE

Comprehensive analysis of acetylcholinesterase inhibitor and reactivator complexes: implications for drug design and antidote development W. Bagrowska, A. Karasewicz, A. Góra, Drug Discovery Today, vol. 29, no. 12, p. 104217, 2024, Oct 29, DOI: https://doi.org/10.1016/j.drudis.2024.104217 ARTICLE

Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane‐bound cytochrome P450 2B4 S. B. Han, J. Teuffel, G. Mukherjee, R. C. Wade, Protein Science, vol. 33, no. 10, 2024, Sep 18, DOI: https://doi.org/10.1002/pro.5165 ARTICLE

Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase F. Sohraby, A. Nunes-Alves, J. Chem. Inf. Model., vol. 64, no. 10, pp. 4193–4203, 2024, May 10, DOI: https://doi.org/10.1021/acs.jcim.4c00187 ARTICLE

Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases C.E. Sequeiros-Borja, B. Surpeta, A. S. Thirunavukarasu, C. J. Dongmo Foumthuim, I. Marchlewski, J. Brezovsky, J. Chem. Inf. Model., vol. 64, no. 15, pp. 6014–6025, 2024 Apr 26, DOI: https://doi.org/10.1021/acs.jcim.4c00094 ARTICLE

Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration S. M. Kim, S. H. Kang, B. W. Jeon, Y. H. Kim, Bioresource Technology, vol. 394, p. 130248, 2024, Feb, DOI: https://doi.org/10.1016/j.biortech.2023.130248 ARTICLE

2023

The proteolytic cleavage of TLR8 Z-loop by furin protease – molecular recognition, reaction mechanism and role of water molecules M. Bzówka, K. Szleper, A. Stańczak, T. Borowski, A. Góra, Springer Science and Business Media LLC, 2023, Nov 14, DOI: https://doi.org/10.21203/rs.3.rs-3590328/v1 ARTICLE

2022

Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls K. Mitusińska, M. Bzówka, T. Magdziarz, A. Góra, J. Chem. Inf. Model., vol. 62, no. 24, pp. 6803–6811, 2022, Nov 14, DOI: https://doi.org/10.1021/acs.jcim.2c00985 ARTICLE

The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s S. Meng, Y. Ji, L. Zhu, G. V. Dhoke, M. D. Davari, U. Schwaneberg, Biotechnology Advances, vol. 61, p. 108051, 2022, Oct 18, DOI: https://doi.org/10.1016/j.biotechadv.2022.108051 ARTICLE

Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases? M. Bzówka, K. Mitusińska, A. Raczyńska, T. Skalski, A. Samol, W. Bagrowska, T. Magdziarz, A. Góra, PLoS Comput Biol, vol. 18, no. 5, p. e1010119, 2022 May 17, DOI: https://doi.org/10.1371/journal.pcbi.1010119 ARTICLE

Toward wide-spectrum antivirals against coronaviruses: Molecular characterization of SARS-CoV-2 NSP13 helicase inhibitors G. R. Perez-Lemus, C. A. Menéndez, W. Alvarado, F. Byléhn, J. J. de Pablo, Sci. Adv., vol. 8, no. 1, 2022, Jan 7, DOI: https://doi.org/10.1126/sciadv.abj4526 ARTICLE

2021

TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them J. Brezovsky, A.S. Thirunavukarasu, B. Surpeta, C.E. Sequeiros-Borja, N. Mandal, D.K. Sarkar, C.J.D. Foumthuim, N. Agrawal, Bioinformatics, vol. 38, no. 6, pp. 1752–1753, 2021, Dec 31, DOI: https://doi.org/10.1093/bioinformatics/btab872 ARTICLE

Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network K. Mitusińska, P. Wojsa, M. Bzówka, A. Raczyńska, W. Bagrowska, A. Samol, P. Kapica, A. Góra, Computational and Structural Biotechnology Journal, vol. 20, pp. 193–205, 2021 Dec 13, DOI: https://doi.org/10.1016/j.csbj.2021.10.042 ARTICLE

Functional Dynamics of an Ancient Membrane-Bound Hydrogenase M. E. Mühlbauer, A. P. Gamiz-Hernandez, V. R. I. Kaila, J. Am. Chem. Soc., vol. 143, no. 49, pp. 20873–20883, 2021, Nov 30, DOI: https://doi.org/10.1021/jacs.1c09356 ARTICLE

Computational insights into the known inhibitors of human soluble epoxide hydrolase M. Bzówka, K. Mitusińska, K. Hopko, A. Góra, Drug Discovery Today, vol. 26, no. 8, pp. 1914–1921, 2021, Aug 27, DOI: https://doi.org/10.1016/j.drudis.2021.05.017 ARTICLE

AQUA-DUCT: Analysis of Molecular Dynamics Simulations of Macromolecules with the use of Molecular Probes [Article v1.0] K. Mitusińska, A. Raczyńska, P. Wojsa, M. Bzówka, A. Góra, Living J. Comp. Mol. Sci., vol. 2, no. 1, p. 21383, 2021, Mar 8, DOI: https://doi.org/10.33011/livecoms.2.1.21383 ARTICLE

Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2 A. Fischer, M. Sellner, K. Mitusińska, M. Bzówka, M. A. Lill, A. Góra, IJMS, vol. 22, no. 4, p. 2065, 2021, Feb 19, DOI: https://doi.org/10.3390/ijms22042065 ARTICLE

Tunnel Engineering for Modulating the Substrate Preference in Decarbonylase P450BsβHI Shuaiqi Meng, Ruipeng An, Zhongyu Li et al. , PREPRINT (Version 2) available at Research Square, 2021, Jan 27, DOI: https://doi.org/10.21203/rs.3.rs-132813/v2 ARTICLE

2020

Structural and Evolutionary Analysis Indicate that the SARS-CoV-2 Mpro is an Inconvenient Target for Small-Molecule Inhibitors Design M. Bzówka, K. Mitusińska, A. Raczyńska, A. Samol, J. A. Tuszyński, A. Góra, openRxiv, 2020, Mar 02, DOI: https://doi.org/10.1101/2020.02.27.968008 ARTICLE

Potential of pyrroquinazoline alkaloids from Adhatoda vasica Nees. as inhibitors of 5-LOX – a computational and an in-vitro study Prasanth Ghanta, S. Sinha, M. Doble, B. Ramaiah, J. Biomol. Struct. Dyn. 2020, Nov 23;1-12 DOI: https://doi.org/10.1080/07391102.2020.1848635 ARTICLE

Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases D. Sivakumar, V. Kumar, M. Naumann, M. Stein, Journal of Biological Chemistry, vol. 295, no. 20, pp. 6972–6982, May 2020, DOI: https://doi.org/10.1074/jbc.RA120.013073 ARTICLE

Novel Potential Binding Sites for Selective Inhibitor Design of Human Soluble Epoxide Hydrolase M. Bzówka, K. Mitusińska, A. Góra, Springer Science and Business Media LLC, 2020, May 23, DOI: https://doi.org/10.21203/rs.3.rs-29814/v1 ARTICLE

Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering B. Surpeta, C.E. Sequeiros-Borja, J. Brezovsky, Int. J. Mol. Sci. 2020, 21, 2713. DOI: https://doi.org/10.3390/ijms21082713 ARTICLE

Water-Intake and Water-Molecule Paths to the Active Site of Secretory Phospholipase A₂ Studied Using MD Simulations and the Tracking Tool AQUA-DUCT H.D. Tjørnelund, J.J. Madsen, G.H.J. Peters, J. Phys. Chem. B2020, 124, 10, 1881-1891 DOI: https://doi.org/10.1021/acs.jpcb.9b10837 ARTICLE

2019

AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective T. Magdziarz, K. Mitusińska, M. Bzówka, A. Raczyńska, A. Stańczak, M. Banas, W. Bagrowska, A. Góra Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2599–2601. DOI: https://doi.org/10.1093/bioinformatics/btz946 ARTICLE

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase
K. Subramanian, K. Mitusińska, J. Raedts, F. Almourfi, H. J. Joosten, S. Hendriks, S. E. Sedelnikova, S. W. M. Kengen, W. R. Hagen, A. Góra, V.A. P. Martins dos Santos, P. J. Baker, J. van der Oost, P. J. Schaap, Biomolecules, 9(6), 212, 2019 DOI: 10.3390/biom9060212 ARTICLE

Engineering enzyme access tunnels
P. Kokkonen, D. Bednar, G. Pinto, Z. Prokop, J. Damborsky, Biotechnology Advances, 2019, DOI: 10.1016/j.biotechadv.2019.04.008 ARTICLE

Chemoinformatics: From Chemical Art to Chemistry in Silico
J. Polanski, Encyclopedia of Bioinformatics and Computational Biology, 601-618, 2019, DOI: 10.1016/b978-0-12-809633-8.20189-1 ARTICLE

2018

Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking
K. Mitusińska, T. Magdziarz, M. Bzówka, A. Stańczak, A. Gora, Biomolecules, 8(4), 143, (2018), DOI: 10.3390/biom8040143 ARTICLE

Self-Assembly Simulations of Classic Claudins—Insights into the Pore Structure, Selectivity, and Higher Order Complexes
F. J. Irudayanathan, X. Wang, N. Wang,S. R. Willsey, I. A. Seddon, S. Nangia , J. Phys. Chem. B, Article ASAP DOI: 10.1021/acs.jpcb.8b03842 ARTICLE

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access.
K. Subramanian, A. Góra, R. Spruijt, K. Mitusińska, M. Suarez-Diez, V. M. dos Santos, P. J. Schaap, PLoS ONE 13(6): e0198990. DOI: 10.1371/journal.pone.0198990 ARTICLE^{Open Access}

2017

Chemoinformatics: From Chemical Art to Chemistry In Silico
J.Polański, University of Silesia, Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, (2017) DOI: 10.1016/B978-0-12-409547-2.14327-6 ARTICLE

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics
V. Vad, J. Byška, A. Jurcík, I. Viola, E. M. Gröller, H. Hauser, S. M. Marques, J. Damborský, B. Kozlíková . Eurographics Workshop on Visual Computing for Biology and Medicine (2017) DOI: 10.2312/vcbm.20171235 ARTICLE