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2019
fmb 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).
plumID:19.008
open access
jp 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).
jp 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).
glycob2 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
jsbmb 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).
bmcg 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).
open access
galectin 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).
open access

2017
phyto V. Spiwok
Protein-Ligand Docking and its Place in Structure-Based Drug Design
ФАРМАЦЕВТИЧЕСКИЙ БЮЛЛЕТЕНЬ 1-4 12-19 (2017).
fg2 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).
plumID:19.006
chpi3 V. Spiwok
CH/π Interactions in Carbohydrate Recognition
Molecules 22(7) 1038 (2017).
open access
altruistic2 P. Hošek, P. Kříž, D. Toulcová & V. Spiwok
Multisystem Altruistic Metadynamics – Well-Tempered Variant
Journal of Chemical Physics 146 125103 (2017).
close 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
jecmen 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)
open access
mpmv 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).
matrix 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).
JCTC 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).
open access
BMCL 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).
JPCB P. Hošek, D. Toulcová, A. Bortolato & V. Spiwok
Altruistic Metadynamics: Multisystem Biased Simulation
Journal of Physical Chemistry B 120(9) 2209-2215 (2016).
CPC 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
slovnik Kolektiv autorů pod vedením prof. Kodíčka
Slovník chemických pojmů aneb Chemické pomněnky (aplikace pro OS Android)
Get it on Google Play
BP P. Hošek & V. Spiwok
Už jste vyzkoušeli Metadyn View?
Bioprospect 25 51-53 (2015).
open access
JCTC 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).
CR 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).
open access
CR 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).
CR 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).
BA V. Spiwok, P. Hošek & Z. Šućur
Enhanced Sampling Techniques in Biomolecular Simulations
Biotechnology Advances 6 pt 2 1130-1140 (2015).

2014
JV 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).
BJ 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).
BP 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).
OBC2 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).
open access
CBDD 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
JCPC2 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).
JCPB 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).
JMCBE 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
JCIM 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
JCP V. Spiwok & B. Králová
Metadynamics in the Conformational Space Nonlinearly Dimensionally Reduced by Isomap.
Journal of Chemical Physics 135 224504 (2011).    ON THE COVER
JPCC 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).
PCCP 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).
MROC V. Spiwok
Editorial [Hot Topic: Computational Glycochemistry and Glycobiology (Guest Editor: Vojtech Spiwok)].
Mini-Reviews in Organic Chemistry 8 221 (2011).
MROC V. Spiwok & A. D. French
Modelling the Effect of Solvents on Carbohydrates.
Mini-Reviews in Organic Chemistry 8 249-255 (2011).
Chem Eur J 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).
Plant Science 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
Biochemistry 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).
Carbohydrate Research 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).
Organic and Biomolecular Chemistry 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
Carbohydrate Research V. Spiwok & I. Tvaroška
Metadynamics Modelling of the Solvent Effect on Primary Hydroxyl Rotamer Equilibria in Hexopyranosides.
Carbohydrate Research 344 1575-1581 (2009).
Journal of Physical Chemistry B 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
Journal of Molecular Modeling 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).
Chemistry 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).
Journal of Organometallic Chemistry 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
Journal of Physical Chemistry B 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).
Journal of Organometallic Chemistry 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).
Journal of Molecular Modeling 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
Journal of Computer-Aided Molecular Design 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
Journal of Molecular Biology 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).
Collection of Czech Chemical Communications 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
Carbohydrate Research 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
Enzyme and Microbial Technology 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).