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2024

	F. Li et al. CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein Journal of Chemical Information and Modeling accepted (2024).
	J. Beránek, A. Křenek & V. Spiwok Analysis of metadynamics simulations by metadynminer.py Bioinformatics 40(10) btae614 (2024).
	A. Chayka, M. Danda, A. Dostálková, V. Spiwok, A. Klimešová, M. Kapisheva, M. Zgarbová, J. Weber, T. Ruml, M. Rumlová & Z. Janeba Developing Allosteric Inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase ChemMedChem accepted (2024).
	P. Kříž, J. Beránek & V. Spiwok Uncertainties of Predictions from Temperature Replica Exchange Simulations Journal Chemical Physics 160 184116 (2024).
	M. Kurfiřt, V. Hamala, J. Beránek, L. Červenková Šťastná, J. Červený, M. Dračínský, J. Bernášková, V. Spiwok, Z. Bosáková, P. Bojarová & J. Karban Synthesis and unexpected binding of monofluorinated N,N'-diacetylchitobiose and LacdiNAc to wheat germ agglutinin Bioorganic Chemistry 147 107395 (2024).
	H. Hradiská, M. Kurečka, J. Beránek, G. Tedeschi, V. Višňovský, A. Křenek & V. Spiwok Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics Journal of Physical Chemistry B 128(4) 903-913 (2024).

2023

	V. Finger, T. Kucera, R. Kafkova, L. Muckova, R. Dolezal, J. Kubes, M. Novak, L. Prchal, L. Lakatos, M. Andrs, M. Hympanova, J. Marek, M. Kufa, V. Spiwok, O. Soukup, E. Mezeiova, J. Janousek, L. Nevosadova, M. Benkova, R.R.A. Kitson, M. Kratky, S. Bosze, K. Mikusova, R. Hartkoorn, J. Roh & J. Korabecny 2,6-Disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines as a new class of potent antitubercular agents inhibiting DprE1 European Journal of Medicinal Chemistry 258 115611 (2023).
	P. Kříž, J. Beránek & V. Spiwok Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Journal of Chemical Theory and Computation 19(7) 2102-2108 (2023).

2022

	D. Trapl & V. Spiwok Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d R Journal 14(3) 46-58 (2022).
	V. Spiwok, M. Kurečka & A. Křenek Collective Variable for Metadynamics Derived from AlphaFold Output Frontiers in Molecular Biosciences 9 878133 (2022).
	D. Trapl, M. Krupička, V. Višňovský, J. Hozzová, J. Oľha, A. Křenek & V. Spiwok Property map collective variable as a useful tool for force field correction Journal of Chemical Information and Modeling 62(3) 567-576 (2022).
	T. Kovaľová, T. Kovaľ, J. Stránský, P. Kolenko, J. Dušková, L. Švecová, P. Vodičková, V. Spiwok, E. Benešová, P. Lipovová & J. Dohnálek The first structure-function study of GH151 α-L-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity FEBS Journal 289(16) 4998-5020 (2022). ON THE COVER

2021

	I. Walsh, D. Fishman, D. Garcia-Gasulla, T. Titma, G. Pollastri, ELIXIR Machine Learning Focus Group, J. Harrow, F. E. Psomopoulos & S. C. E. Tosatto DOME: Recommendations for supervised machine learning validation in biology Nature Methods 18 1122-1127 (2021).
	T. Přerovská, A. Pavlů, D. Hancharyk, A. Rodionova, A. Vavříková & V. Spiwok Structural basis of the function of Yariv reagent – An important tool to study arabinogalactan proteins Frontiers in Molecular Biosciences 8 682858 (2021).
	J. Bejček, M. Jurášek, V. Spiwok, & S. Rimpelová Quo vadis cardiac glycoside research? Toxins 13 344 (2021).
	J. Bejček, V. Spiwok, E. Kmoníčková & S. Rimpelová Na⁺/K⁺-ATPase revisited: On its mechanism of action, role in cancer, and relevant inhibitors Molecules 26(7) 1905 (2021).
	E. Benešová, Z. Šućur, M. Těšínský, V. Spiwok & P. Lipovová Transglycosylation abilities of β-D-galactosidases from GH family 2 3 Biotech 11 168 (2021).
	J. Bejček, V. Spiwok, E. Kmoníčková, T. Ruml & S. Rimpelová Kardioglykosidy: terapeutický potenciál pro léčbu nádorových onemocnění Chemické Listy 115 4-12 (2021).
	T. Přerovská, S. Henke, R. Bleha, V. Spiwok, S. Gillarová, J.-C. Yvin, V. Ferrières, E. Nguema-Ona, P. Lipovová Arabinogalactan-like glycoproteins from Ulva lactuca (Chlorophyta) show unique features compared to land plants AGPs Journal of Phycology 57(2) 619-635 (2021).
	M. Zanin et al. An early stage researcher's primer on systems medicine terminology Network and Systems Medicine 4(1) 2-50 (2021).
	H. Wang et al. Deep Learning in Systems Medicine Briefings in Bioinformatics 22(2) 1543-1559 (2021).

2020

	D. Trapl, C. Cuerdo del Río, P. Kříž & V. Spiwok Prediction of pKa in a System with High Orthogonal Barriers: Alchemical Flying Gaussian Method Chemical Physics Letters 760 138012 (2020).
	K.T. Gurwitz et al. A framework to assess the quality and impact of bioinformatics training across ELIXIR PLOS Computational Biology 16(7) e1007976 (2020).
	V. Spiwok & P. Kříž Time-lagged t-distributed stochastic neighbor embedding (t-SNE) of molecular simulation trajectories Frontiers in Molecular Biosciences 7 132 (2020).
	T. Vašíček, V. Spiwok, J. Červený, L. Petrásková, L. Bumba, D. Vrbata, H. Pelantová, V. Křen & P. Bojarová Regioselective 3-O-substitution of unprotected thiodigalactosides: Direct route to galectin inhibitors Chemistry — A European Journal 26(43) 9620-9631 (2020).

2019

	C. O. Solanke, D. Trapl, Z. Šućur, V. Mareška, I. Tvaroška & V. Spiwok Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain Scientific Reports 9 18918 (2019).
	V. Pavlíčková, S. Rimpelová, M. Jurášek, K. Záruba, J. Fähnrich, I. Křížová, J. Bejček, Z. Rottnerová, V. Spiwok, P. Drašar & T. Ruml PEGylated purpurin 18 with improved solubility: Potent compounds for photodynamic therapy of cancer Molecules 24(24), 4477 (2019).
	G. Verkhivker, F.L. Gervasio & V. Spiwok Editorial: Machine Learning in Biomolecular Simulations Frontiers in Molecular Biosciences 6, 76 (2019).
	S. Rimpelová, M. Jurášek, L. Peterková, J. Bejček, V. Spiwok, M. Majdl, M. Jirásko, M. Buděšínský, J. Harmatha, E. Kmoníčková, P. Drašar, T. Ruml Archangelolide: Sesquiterpene lactone with immunobiological potential from Laserpitium archangelica Beilstein Journal of Organic Chemistry 15, 1933-1944 (2019).
	PLUMED Consortium Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods 16 667-673 (2019).
	D. Trapl, I. Horvaćanin, V. Mareška, F. Özçelik, G. Unal & V. Spiwok anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations Frontiers in Molecular Biosciences 6, 25 (2019).
	F. L. Gervasio, V. Spiwok, R. Mannhold (Editors), H. Buschmann, J. Holenz (Series Editors) Biomolecular Simulations in Structure-Based Drug Discovery (Methods and Principles in Medicinal Chemistry) 1st Edition (2019).
	L. Hernychová, M. Rosůlek, A. Kádek, V. Mareška, J. Chmelík, L. Adámková, V. Grobárová, O. Šebesta, Z. Kukačka, K. Skála, V. Spiwok, J. Černý & P. Novák The C-type lectin-like receptor Nkrp1b: structural proteomics reveals features affecting protein conformation and interactions Journal of Proteomics 196 162-172 (2019).
	T. Kovaľová, T. Kovaľ, E. Benešová, P. Vodičková V. Spiwok, P. Lipovová & J. Dohnálek Active Site Complementation and Hexameric Arrangement in the GH Family 29: A Structure-Function Study of α-L-Fucosidase Isoenzyme 1 from Paenibacillus thiaminolyticus Glycobiology 29(1) 59-73 (2019).

2018

	M. Jurášek, M. Černohorská, J. Řehulka, V. Spiwok, T. Sulimenko, E. Dráberová, M. Darmostuk, S. Gurská, I. Frydrych, R. Buriánová, T. Ruml, M. Hajdúch, P. Bartůněk, P. Dráber, P. Džubák, P. B. Drašar & D. Sedlák Estradiol Dimer Inhibits Tubulin Polymerization and Microtubule Dynamics Journal of Steroid Biochemistry and Molecular Biology 183 68-79 (2018).
	A. Janská, P. Svoboda, V. Spiwok, L. Kučera & J. Ovesná The Dehydration Stress of Couch Grass is Associated with its Lipid Metabolism, the Induction of Transporters and the Reprogramming of Development Coordinated by ABA BMC Genomics 19 317 (2018).
	L. Bumba, D. Laaf, V. Spiwok, L. Elling, V. Křen & P. Bojarová Poly-N-acetyllactosamine Neo-Glycoproteins as Nanomolar Ligands of Human Galectin-3: Binding Kinetics and Modeling International Journal of Molecular Sciences 19(2) 372 (2018).

2017

	V. Spiwok Protein-Ligand Docking and its Place in Structure-Based Drug Design ФАРМАЦЕВТИЧЕСКИЙ БЮЛЛЕТЕНЬ 1-4 12-19 (2017).
	P. Kříž, Z. Šućur & V. Spiwok Free Energy Surface Prediction by Flying Gaussian Method: Multi-System Representation Journal of Physical Chemistry B 121(46) 10479-10483 (2017).
	V. Spiwok CH/π Interactions in Carbohydrate Recognition Molecules 22(7) 1038 (2017).
	P. Hošek, P. Kříž, D. Toulcová & V. Spiwok Multisystem Altruistic Metadynamics – Well-Tempered Variant Journal of Chemical Physics 146 125103 (2017).
	J. Pazúriková, A. Křenek, V. Spiwok & M. Šimková Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics Journal of Chemical Physics 146 115101 (2017).

2016

	P. Svoboda, A. Janská, V. Spiwok, I.T. Prášil, K. Kosová, P. Vítámvás & J. Ovesná Global Scale Transcriptional Profiling of Two Contrasting Barley Genotypes Exposed to Moderate Drought Conditions: Contribution of Leaves and Crowns to Water Shortage Coping Strategies Frontiers in Plant Science 7 1958 (2016)
	T. Kroupa, H. Langerová, M. Doležal, J. Prchal, V. Spiwok, E. Hunter, M. Rumlová, R. Hrabal & T. Ruml Membrane Interactions of the Mason-Pfizer Monkey Virus Matrix Protein and its Budding Deficient Mutants Journal of Molecular Biology 228(23) 4708-4722 (2016).
	P. Junková, J. Prchal, V. Spiwok, R. Pleskot, J. Kadlec, L. Krásný, R. Hynek, R. Hrabal & T. Ruml Molecular Aspects of the Interaction Between Mason-Pfizer Monkey Virus Matrix Protein and Artificial Phospholipid Membrane Proteins: Structure, Function, and Bioinformatics 84(11) 1717-1727 (2016).
	Z. Šućur & V. Spiwok Sampling Enhancement and Free Energy Prediction by Flying Gaussian Method Journal of Chemical Theory and Computation 12(9) 4644-4650 (2016).
	I. Chlubnová, B. Králová, H. Dvořáková, V. Spiwok, D. Filipp, C. Nugier-Chauvin, R. Daniellou & V. Ferrières Biocatalyzed Synthesis of Difuranosides and their Ability to Trigger Production of TNF-α Bioorganic & Medicinal Chemistry Letters 26(6) 1550-1553 (2016).
	P. Hošek, D. Toulcová, A. Bortolato & V. Spiwok Altruistic Metadynamics: Multisystem Biased Simulation Journal of Physical Chemistry B 120(9) 2209-2215 (2016).
	P. Hošek & V. Spiwok Metadyn View: Fast Web-Based Viewer of Free Energy Surfaces Calculated by Metadynamics Computer Physics Communications 198 222-229 (2016).	try it!

2015

	Kolektiv autorů pod vedením prof. Kodíčka Slovník chemických pojmů aneb Chemické pomněnky (aplikace pro OS Android)
	P. Hošek & V. Spiwok Už jste vyzkoušeli Metadyn View? Bioprospect 25 51-53 (2015).
	S. Haldar, P. Kührová, P. Banáš, V. Spiwok, J. Šponer, P. Hobza & M. Otyepka Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microseconds Molecular Dynamics and Well Tempered Metadynamics Journal of Chemical Theory and Computation 11(8) 3866-3877 (2015).
	E. Benešová, P. Lipovová, J. Krejzová, T. Kovaľová, P. Buchtová, V Spiwok & B. Králová α-L-Fucosidase Isoenzyme iso2 from Paenibacillus thiaminolyticus BMC Biotechnology 15 36 (2015).
	V. Spiwok, P. Oborský, J. Pazúriková, A. Křenek & B. Králová Nonlinear vs. Linear Biasing in Trp-cage Folding Simulations Journal of Chemical Physics 142 115101 (2015).
	V. Mareška, I. Tvaroška, B. Králová & V. Spiwok Molecular Simulations of Hevein/(GlcNAc)₃ Complex with Weakened OH/O and CH/π Hydrogen Bonds: Implications for their Role in Complex Stabilization Carbohydrate Research 408 1-7 (2015).
	V. Spiwok, P. Hošek & Z. Šućur Enhanced Sampling Techniques in Biomolecular Simulations Biotechnology Advances 6 pt 2 1130-1140 (2015).

2014

	K. Strohalmová-Bohmová, V. Spiwok, M. Lepšík, R. Hadravová, I. Křížová, P. Ulbrich, I. Pichová, L. Bednář, T. Ruml & M. Rumlová Role of Mason-Pfizer monkey virus CA-NC spacer peptide-like domain in assembly of immature particles Journal of Virology 88(24) 14148-14160 (2014).
	M.A. Corral-Rodríguez, M. Stuiver, G. Abascal-Palacios, T. Diercks, I. Oyenarte, J. Ereño-Orbea, A. Ibáñez De Opakua, F.J. Blanco, J.A. Encinar, V. Spiwok, H. Terashima, A. Accardi, D. Müller & L.A. Martinez-Cruz Nucleotide Binding Triggers a Conformational Change of the CBS Module of the Magnesium Transporter CNNM2 from a Twisted towards a Flat Structure. Biochemical Journal 464(1) 23-34 (2014).
	V. Pliška, G. Folkers & V. Spiwok Thermodynamics of the Interaction Between Oxytocin and its Myometrial Receptor in Sheep: A Stepwise Binding Mechanism Biochemical Pharmacology 91 119-127 (2014).
	I. Chlubnová, B. Králová, H. Dvořáková, P. Hošek, V. Spiwok, D. Filipp, C. Nugier-Chauvin, R. Daniellou & V. Ferrières The versatile enzyme Araf51 allowed efficient synthesis of rare pathogen-related β-D-galactofuranosyl-pyranoside disaccharides. Organic & Biomolecular Chemistry 12 3080-3089 (2014).
	A. Macurkova, T. Neubauerova, K. Poncova, R. Jezek, P. Lovecka, V. Spiwok, M. Mackova & T. Macek Effect of Chain Elongation on Biological Properties of the Toxin Paralysin β-Alanyl-tyrosine. Chemical Biology & Drug Design 84 418-426 (2014).

2013

	S. Haldar, V. Spiwok & P. Hobza On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations. Journal of Physical Chemistry C 117 11066-11075 (2013).
	P. Oborský, I. Tvaroška, B. Králová, V. Spiwok Toward an Accurate Conformational Modeling of Iduronic Acid. Journal of Physical Chemistry B 117 1003-1009 (2013).
	J. Krejzová, P. Šimon, E. Vavříková, K. Slámová, H. Pelantová, S. Riva, V. Spiwok & V. Křen Enzymatic Synthesis of New C-6-Acylated Derivatives of NAG-Thiazoline and Evaluation of their Inhibitor Activities Towards Fungal β-N-Acetylhexosaminidase. Journal of Molecular Catalysis B: Enzymatic 87 128-134 (2013).

2012

V. Spiwok, K. Hlat-Glembová, I. Tvaroška & B. Králová
Conformational Free Energy Modeling of Drug-Like Molecules by Metadynamics in the WHIM Space.
Journal of Chemical Information and Modeling 52 804-813 (2012).

2011

	V. Spiwok & B. Králová Metadynamics in the Conformational Space Nonlinearly Dimensionally Reduced by Isomap. Journal of Chemical Physics 135 224504 (2011). ON THE COVER
	V. Spiwok, P. Hobza & J. Řezáč Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface. Journal of Physical Chemistry C 115 19455-19462 (2011).
	S. Kozmon, R. Matuška, V. Spiwok & J. Koča Dispersion Interactions of Carbohydrates with Condensate Aromatic Moieties: Theoretical Study on the CH-π Interaction Additive Properties. Physical Chemistry Chemical Physics 13 14215-14222 (2011).
	V. Spiwok Editorial [Hot Topic: Computational Glycochemistry and Glycobiology (Guest Editor: Vojtech Spiwok)]. Mini-Reviews in Organic Chemistry 8 221 (2011).
	V. Spiwok & A. D. French Modelling the Effect of Solvents on Carbohydrates. Mini-Reviews in Organic Chemistry 8 249-255 (2011).
	S. Kozmon, R. Matuška, V. Spiwok & J. Koča Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/π Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods. Chemistry — A European Journal 17 5680-5690 (2011).
	T. Podzimek, J. Matoušek, P. Lipovová, P. Poučková, V. Spiwok & J. Šantrůček Biochemical Properties of Three Plant Nucleases with Anticancer Potential. Plant Science 180 343-351 (2011).

2010

	A. Hnízda, V. Spiwok, V. Jurga, V. Kožich, M. Kodíček & J. P. Kraus Cross-Talk between the Catalytic Core and the Regulatory Domain in Cystathionine β-Synthase: Study by Differential Covalent Labeling and Computational Modeling. Biochemistry 49 10526-10534 (2010).
	V. Spiwok, B. Králová & I. Tvaroška Modelling of β-D-Glucopyranose Ring Distortion in Different Force Fields: A Metadynamics Study. Carbohydrate Research 335 530-537 (2010).
	I. Chlubnová, D. Filipp, V. Spiwok, H. Dvořáková, R. Daniellou, C. Nugier-Chauvin, B. Králová & V. Ferrières Enzymatic Synthesis of oligo-D-Galactofuranosides and L-Arabinofuranosides: From Molecular Dynamics to Immunological Assays. Organic and Biomolecular Chemistry 8 2092-2102 (2010).

2009

	V. Spiwok & I. Tvaroška Metadynamics Modelling of the Solvent Effect on Primary Hydroxyl Rotamer Equilibria in Hexopyranosides. Carbohydrate Research 344 1575-1581 (2009).
	V. Spiwok & I. Tvaroška Conformational Free Energy Surface of α-N-Acetylneuraminic Acid: An Interplay Between Hydrogen Bonding and Solvation. Journal of Physical Chemistry B 113 9589-9594 (2009). ON THE COVER

2008

	V. Spiwok, B. Králová & I. Tvaroška Continuous Metadynamics in Essential Coordinates as a Tool for Free Energy Modelling of Conformational Changes. Journal of Molecular Modeling 14 995-1002 (2008).
	H. Valdes, V. Spiwok, J. Rezac, D. Reha, A.G. Abo-Riziq, M.S. de Vries & P. Hobza Potential-Energy and Free-Energy Surfaces of Glycyl-Phenylalanyl-Alanine (GFA) Tripeptide: Experiment and Theory. Chemistry — A European Journal 14 4886-4898 (2008).
	D. Desbouis, H. Struthers, V. Spiwok, T. Kuster & R. Schibli Synthesis, In Vitro, and In Silico Evaluation of Organometallic Technetium and Rhenium Thymidine Complexes with Retained Substrate Activity Toward Human Thymidine Kinase Type 1 Journal of Medicinal Chemistry 51 6689-6698 (2008).

2007

	V. Spiwok, P. Lipovová & B. Králová Metadynamics in Essential Coordinates: Free Energy Simulation of Conformational Changes. Journal of Physical Chemistry B 111 3073-3076 (2007).
	M. Stichelberger, D. Desbouis, V. Spiwok, L. Scapozza, P.A. Schubiger & R. Schibli Synthesis, In Vitro and In silico Assessment of Organometallic Rhenium(I) and Technetium(I) Thymidine Complexes. Journal of Organometallic Chemistry 692 1255-1264 (2007).
	V. Spiwok, P. Lipovová, T. Skálová, J. Dušková, J. Dohnálek, J. Hašek, N. J. Russell & B. Králová Cold-Active Enzymes Studied by Comparative Molecular Dynamics Simulation. Journal of Molecular Modeling 13 485-497 (2007).

2005

	V. Spiwok, P. Lipovová, T. Skálová, E. Vondráčková, J. Dohnálek, J. Hašek & B. Králová Modelling of Carbohydrate-Aromatic Interactions: Ab Initio Energetics and Force Field Performance. Journal of Computer-Aided Molecular Design 19 887-901 (2005). SUPPLEMENTARY MATERIAL
	T. Skálová, J. Dohnálek, V. Spiwok, P. Lipovová, E. Vondráčková, H. Petroková, J. Dušková, H. Strnad, B. Králová & J. Hašek Cold-active β-Galactosidase from Arthrobacter sp. C2-2 Forms Compact 660 kDa Hexamers: Crystal Structure at 1.9 Å Resolution. Journal of Molecular Biology 353 282-294 (2005).
	H. Petroková, E. Vondráčková, T. Skálová, J. Dohnálek, P. Lipovová, V. Spiwok, H. Strnad, B. Králová & J. Hašek Crystallization and Preliminary X-Ray Diffraction Analysis of Cold-Active β-Galactosidase from Arthrobacter sp. C2-2. Collection of Czech Chemical Communications 70 124-132 (2005).

2004

V. Spiwok, P. Lipovová, T. Skálová, E. Buchtelová, J. Hašek & B. Králová
Role of CH/π Interactions in Substrate Binding by Escherichia coli β-Galactosidase.
Carbohydrate Research 339 2275-2280 (2004).

2003

P. Karasová-Lipovová, H. Strnad, V. Spiwok, Š. Malá, B. Kralová, N.J. Russell
The Cloning, Purification and Characterisation of a Cold-Active β-Galactosidase from the Psychrotolerant Antarctic Bacterium Arthrobacter sp. C2-2.
Enzyme and Microbial Technology 33 836-844 (2003).