Publications
2018
CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories., Bioinformatics, bty386, 2018. | :
Computational Analysis of Protein Tunnels and Channels, Protein Engineering: Methods and Protocols, Methods in Molecular Biology, Uwe T. Bornscheuer and Matthias Hohne (eds.),, vol. 1685, pp 25-42, 2018, 978-1-4939-7364-4. | :
2016
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(3), 2016. | :
2014
CAVER Analyst 1.0: Graphic Tool for Interactive Visualization and Analysis of Tunnels and Channels in Protein Structures, Bioinformatics, 30(18), 2014. | :
2013
CAVER Analyst - Engineering Enzymes by Modification Of Access Tunnels, poster at Biotrans, 2013. | :
Method of Thermostabilization of a Protein and/or Stabilization Towards Organic Solvents, Masaryk University, Brno, Czech Republic. Patent US 8,580,932, 2013. | :
Software Tools for Identification, Visualization and Analysis of Protein Tunnels and Channels, Biotechnology Advances , 31, 38-49, 2013. | :
Gates of Enzymes, Chemical Reviews, 113, 5871–5923, 2013. | :
2012
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures, PLoS Computational Biology 8: e1002708, 8(10), 2012. | :
2011
CAVER 3.0, software, 2011. | :
2010
CAVER 2.1, software, 2010. | :
Tracking single channel in protein dynamics, WSCG Communication Papers proceedings, 109-114, 2010, ISBN 978-80-86943-87-9. | :
CAVER Viewer - new tool enhancing computation and visualization of channels in proteins, IADIS Computer Graphics, Visualization, Computer Vision and Image Processing (CGVCVIP), 2010, ISBN 978-972-8939-22-9. | :
2009
Computation of channels in protein dynamics, Proceedings of the IADIS International Conference Applied Computing 2009, IADIS Press Rome, 251-258, 2009, ISBN 978-972-8924-97-3. | :
Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations, Journal of Molecular Biology , 392, 1339-1356, 2009. | :
Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate, Nature Chemical Biology, 5, 727-733, 2009. | :
2008
CAVER 2.0, software, 2008. | :
Computation of more channels in protein molecules, Proceedings Conference Visual Computing For Biomedicine (VCBM), Aire-la-Ville, Switzerland, 45-51, 2008, ISBN 978-3-905674-13-2. | :
Multicriteria Tunnel Computation, CGIM '08 Proceedings of the Tenth IASTED International Conference on Computer Graphics and Imaging, Insbruck, Austria, 160-164, 2008, ISBN 978-0-88986-720-8. | :
2007
Computation of tunnels in protein molecules using Delaunay triangulation, Journal of WSCG, 15(1-3), 107-114, 2007, 978-80-86943-00-8. | :
Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles, Biotechnology Journal, 2, 62-67, 2007. | :
Visualisation of Tunnels in Protein Molecules, AFRIGRAPH '07 Proceedings of the 5th international conference on Computer graphics, virtual reality, visualisation and interaction in Africa, 111-118, 2007, ISBN 978-1-59593-906-7. | :
2006
CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities, BMC Bioinformatics, 7, 316, 2006. | :
2022
Engineering CYP153AM.aq to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening, ChemCatChem, 14, 2022. | :
Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling, JACS Au, 2(6), 1324-1337, 2022. | :
Mechanism-guided tunnel engineering to increase the efficiency of a flavin-dependent halogenase, Nature Catalysis, 5.6, 534-544, 2022. | :
Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies, Biotechnology Advances, 108009, 2022. | :
2021
Engineering the protein dynamics of an ancestral luciferase, Nature Communications, 12, 3616, 2021. | :
Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum, Catalysts, 11(1), 2021. | :
Substrate Anchoring and Flexibility Reduction in CYP153AM.aq Leads to Highly Improved Efficiency toward Octanoic Acid, ACS Catalysis, 11, no. 5, 3182-3189, 2021. | :
Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning, Computational and Structural Biotechnology Journal, 19, 3187-3197, 2021. | :
Web-based tools for computational enzyme design, Current Opinion in Structural Biology, 69, 19-34, 2021. | :
2020
DockVis: Visual Analysis of Molecular Docking Trajectories, Computer Graphics Forum, 36,6, 452-464, 2020. | :
2019
Computational Study of Protein-Ligand Unbinding for Enzyme Engineering, Frontiers in chemistry, 6, 650, 2019. | :
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport, Nucleic acids research, 47, W414-W422, 2019. | :
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization, Computer Graphics Forum, Vol. 38, No. 3, 441-453, 2019. | :
Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock, Frontiers in Chemistry, 7, 709, 2019. | :
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels , Bioinformatics, , 35(23), 4986-4993, 2019. | :
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(5), 1625-1638, 2019. | :
Engineering enzyme access tunnels, Biotechnology advances, 37(6), 107386, 2019. | :
2018
2017
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics., Eurographics Workshop on Visual Computing for Biology and Medicine Proceedings, 36, 33-42, 2017. | :
Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open–Solvated versus Occluded–Desolvated Active Sites., Angewandte Chemie International Edition, 56, 4719-4723, 2017. | :
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling., Journal of Chemical Information and Modeling, 57, 1970-1989, 2017. | :
A Haloalkane Dehalogenase From a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity., Applied and Environmental Microbiology, 84, e01684-17, 2017. | :
Kinetics of Binding of Fluorescent Ligands to Enzymes with Engineered Access Tunnels, FEBS Journal, in press, 2017. | :
NewProt – a Protein Engineering Portal., Protein Engineering, Design & Selection, 30, 441-447, 2017. | :
2016
HotSpot Wizard 2: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering, Nucleic Acids Research, 44, W479-W487, 2016. | :
Engineering a de Novo Transport Tunnel, ACS Catalysis, 6, 7597-7610, 2016. | :
Enzyme Tunnels and Gates as Relevant Targets in Drug Design, Medicinal Research Reviews, in press, 2016. | :
2015
Balancing the Stability-Activity Trade-off by Fine-Tuning Dehalogenase Access Tunnels, ChemCatChem, 7(4), 648–659, 2015. | :
2014
Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design, Nature Chemical Biology, 10, 428–430, 2014. | :
Computational tools for designing and engineering enzymes, Current Opinion in Chemical Biology, 19, 8-16, 2014. | :
2013
2012
A Single Mutation in the Access Tunnel Changes Mechanism of Product Release in Haloalkane Dehalogenase LinB, . Journal of Biological Chemistry , 287, 29062-29074, 2012. | :
2011
Crystallization and Crystallographic Analysis of the Rhodococcus rhodochrous NCIMB 13064 Mutant DhaA31 and its Complex with 1,2,3-Trichloropropane, Acta Crystallographica , 67, 397-400, 2011. | :
2010
Atomic Resolution Studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels, Acta Crystallographica D, 66, 962-969, 2010. | :
Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering, Angewandte Chemie , 49, 6111-6115, 2010. | :
2009
Nanosecond Time-Dependent Stokes Shift at the Tunnel Mouth of Haloalkane Dehalogenases, Journal of the American Chemical Society , 131, 494-501, 2009. | :
Computational Tools for Designing and Engineering Biocatalysts, Current Opinion in Chemical Biology , 13, 26-34, 2009. | :
HotSpot Wizard: A Web Server for Identification of Hot Spots in Protein Engineering, Nucleic Acids Research , 37, W376–W383, 2009. | :
2007
Stepwise Dissection and Visualization of the Catalytic Mechanism of Haloalkane Dehalogenase LinB using Molecular Dynamics Simulations and Computer Graphics, Journal of Molecular Graphics and Modelling , 26, 643-651, 2007. | :
CAVER Analyst | CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories., Bioinformatics, bty386, 2018. | :|
CAVER, CAVER Plugin | CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures, PLoS Computational Biology 8: e1002708, 8(10), 2012. | :
[BibTeX] |
CAVER, CAVER Plugin | CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(3), 2016. | :
[BibTeX] |
CaverDock | CAVERDOCK: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking, In preparation, 2018. | :