AQUA-DUCT citations:

2020

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

Applications of water molecules for analysis of macromolecule properties K Mitusińska, A Raczyńska, M Bzówka, W. Bagrowska, A. Góra, Comput Struct Biotechnol J. 2020; 18: 355–365. DOI: https://doi.org/10.1016/j.csbj.2020.02.001 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 ARTICLEOpen 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