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Publikace ústavu

 

Publikace skupiny Chemoinformatika

  1. McKenna, S. M.; Šícho, M.; van der Horst, C.; Maasland, J.; van der Nol, E.; Turco, G.; Bernatavicius, A.; van Westen, G. J.; Heitman, L. H.; Pomplun, S. J. Automated Parallel Synthesis Accelerates Virtual Screening Hit Discovery. Journal of the American Chemical Society 2026. DOI: 10.1021/jacs.6c05055.
  2. Fil, V.; van den Broek, R. L.; Šícho, M.; Čmelo, I.; Lorente, M. I. A.; Jespers, W.; Van Westen, G. J. P.; Svozil, D. Scaffold-based evaluation metrics for fair comparison of molecular generators. Journal of Cheminformatics 2026, 18 (1), 8-13. DOI: 10.1186/s13321-026-01213-6.
  3. Essa, K.; van der Dussen, K. N.; Yao, Y.; Bleijs, B.; Zacarias, N. V. O.; Heitman, L. H.; van Westen, G. J.; Jespers, W.; van der Es, D.; Šícho, M. Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists. Journal of Chemical Information and Modeling 2025. DOI: 10.1021/acs.jcim.5c01596.
  4. Fülöp, J.; Šícho, M.; Dehaen, W. TEMPL: A Template-Based Protein–Ligand Pose Prediction Baseline. Journal of Chemical Information and Modeling 2025. DOI: 10.1021/acs.jcim.5c01985.
  5. Hassen, A. K.; Šícho, M.; van Aalst, Y. J.; Huizenga, M. C. W.; Reynolds, D. N. R.; Luukkonen, S.; Bernatavicius, A.; Clevert, D.-A.; Janssen, A. P. A.; van Westen, G. J. P.; Preuss, M. Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design. Journal of Cheminformatics 2025. DOI: 10.1186/s13321-024-00910-4.
  6. van den Maagdenberg, H. W.; Šícho, M.; Araripe, D. A.; Luukkonen, S.; Schoenmaker, L.; Jespers, M.; Béquignon, O. J. M.; González, M. G.; van den Broek, R. L.; Bernatavicius, A.; van Hasselt, J. G. C.; van der Graaf, P. H.; van Westen, G. J. P. QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool. Journal of Cheminformatics 2024. DOI: 10.1186/s13321-024-00908-y.
  7. Hunklinger, A.; Hartog, P.; Šícho, M.; Godin, G.; Igor, V Tetko. The openOCHEM consensus model is the best-performing open-source predictive model in the First EUOS/SLAS joint compound solubility challenge. SLAS Discovery 2024. DOI: 10.1016/j.slasd.2024.01.005.
  8. Agea, M.; Čmelo, I.; Dehaen, W.; Chen, Y.; Kirchmair, J.; Sedlák, D.; Bartůněk, P.; Šícho, M.; Svozil, D. Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library. Molecular Informatics 2024. DOI: 10.1002/minf.202300316.
  9. Bernatavicius, A.; Šícho, M.; Janssen, A.; Hassen, A.; Preuss, M.; van Westen, G. AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models. Journal of Chemical Information and Modeling 2024, 64 (21), 8113-8122. DOI: 10.1021/acs.jcim.4c00309.
  10. Šícho, M.; Luukkonen, S.; van den Maagdenberg, H.; Schoenmaker, L.; Béquignon, O.; van Westen, G. DrugEx: Deep Learning Models and Tools for Exploration of Drug-Like Chemical Space. Journal of Chemical Information and Modeling 2023, 63 (12), 3629-3636. DOI: 10.1021/acs.jcim.3c00434.
  11. Šícho, M.; Liu, X.; Svozil, D.; van Westen, G. J. P. GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. Journal of Cheminformatics 2021. DOI: 10.1186/s13321-021-00550-y.
  12. Plonka, W.; Stork, C.; Šícho, M.; Kirchmair, J. CYPlebrity: Machine learning models for the prediction of inhibitors of cytochrome P450 enzymes. BIOORGANIC & MEDICINAL CHEMISTRY 2021. DOI: 10.1016/j.bmc.2021.116388.
  13. NERDD: a web portal providing access to in silico tools for drug discovery. Bioinformatics (Oxford, England) 2020. DOI: 10.1093/bioinformatics/btz695.
  14. Kops, C. D. B.; Šícho, M.; Mazzolari, A.; Kirchmair, J. GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. Chemical Research in Toxicology 2020, 34 (2), 286-299. DOI: 10.1021/acs.chemrestox.0c00224.
  15. GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism. Frontiers in chemistry 2019. DOI: 10.3389/fchem.2019.00402.
  16. Stork, C.; Chen, Y.; Šícho, M.; Kirchmair, J. Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. Journal of Chemical Information and Modeling 2019, 59 (3), 1030-1043. DOI: 10.1021/acs.jcim.8b00677.
  17. Šícho, M.; Stork, C.; Mazzolari, A.; De Bruyn Kops, C.; Pedretti, A.; Testa, B.; Vistoli, G.; Svozil, D.; Kirchmair, J. FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes. Journal of Chemical Information and Modeling 2019, 59 (8), 3400-3412. DOI: 10.1021/acs.jcim.9b00376.
  18. Comment on "The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability". Journal of cheminformatics 2018. DOI: 10.1186/s13321-018-0267-x.
  19. Stork, C.; Wagner, J.; Friedrich, N.-O.; de Bruyn Kops, C.; Šícho, M.; Kirchmair, J. Hit Dexter: A Machine-Learning Model for the Prediction of Frequent Hitters. ChemMedChem 2018, 13 (6), 564-571. DOI: 10.1002/cmdc.201700673.
  20. Molecular docking as a tool to virtually develop drugs. Chemicke Listy 2017, 111, 754-759.
  21. Šícho, M.; Svozil, D. MOLEKULOVÉ DOKOVÁNÍ JAKO NÁSTROJ PRO VIRTUÁLNÍ NÁVRH LÉČIV. Chemické listy 2017, 111 (11), 754-759.
  22. Šícho, M.; Kops, C. D. B.; Stork, C.; Svozil, D.; Kirchmair, J. FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity. Journal of Chemical Information and Modeling 2017, 57 (8), 1832-1846. DOI: 10.1021/acs.jcim.7b00250.
  23. Šícho, M.; Svozil, D.; Hoksza, D. Activity-driven exploration of chemical space with morphing. In Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015; 2015; pp 1024-1031. DOI: 10.1109/BIBM.2015.7359824.

Publikace skupiny Biomolekulární modelování

2026

66. E. Matoušková, M. Cuker, F. Lankaš (2026): Mechanical properties of DNA double-crossover motifs. Submitted. https://www.biorxiv.org/content/10.64898/2026.04.10.717625v1

2025

65. P. Slavníková, M. Cuker, E. Matoušková, I. Čmelo, M. Zgarbová, P. Jurečka, F. Lankaš (2025): Sequence-dependent shape and stiffness of DNA and RNA double helices: hexanucleotide scale and beyond. J. Chem. Inf. Model., 65, 9208-9229, https://doi.org/10.1021/acs.jcim.5c00576

2024

64. H. Dohnalová, E. Matoušková, F. Lankaš (2024): Temperature-dependent elasticity of DNA, RNA and hybrid double helices. Biophys. J., 123, 572-583, https://doi.org/10.1016/j.bpj.2024.01.032

63. H. Dohnalová, M. Seifert, E. Matoušková, M. Klein, F. S. Papini, J. Lipfert, D. Dulin, F. Lankaš (2024): Temperature-dependent twist of double-stranded RNA probed by magnetic tweezer experiments and moleculad dynamics simulations. J. Phys. Chem. B, 128, 664-675, https://doi.org/10.1021/acs.jpcb.3c06280

2023

62. E. Matoušková, M. Růžička, K. Réblová, F. Lankaš (2023): Mechanical properties of DNA double-crossover motif. Published as preprint on bioRxiv, https://biorxiv.org/cgi/content/short/2023.02.28.530469v1

61. E. Matoušková, F. Lankaš (2023): DNA stále trochu záhadná. Vesmír, 102/4, 220-223, https://vesmir.cz/cz/casopis/archiv-casopisu/2023/cislo-4/

2022

60. E. Matoušková, T. Dršata, L. Pfeifferová, J. Šponer, K. Réblová, F. Lankaš (2021): RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems. Biophys. J., 121, 705-714, https://doi.org/10.1016/j.bpj.2022.01.025

2021

59. H. Dohnalová, F. Lankaš (2021): Deciphering the mechanical properties of B-DNA duplex. WIRES Comput. Mol. Sci., e1575, https://doi.org/10.1002/wcms.1575

2020

58. E. Matoušková, E. Bignon, V. Claerbout, T. Dršata, N. Gillet, A. Monari, E. Dumont, F. Lankaš (2020): Impact of the nucleosome histone core on the structure and dynamics of DNA containing pyrimidine-pyrimidone (6-4) photoproduct. J. Chem. Theory Comput., 16, 5972-5981, https://doi.org/10.1021/acs.jctc.0c00593

57. H. Dohnalová, T. Dršata, J. Šponer, M. Zacharias, J. Lipfert, F. Lankaš (2020): Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation. J. Chem. Theory Comput. 16, 2857–2863, https://doi.org/10.1021/acs.jctc.0c00037

56. F. Lankaš (2020): Simple, But Not Too Simple: Modeling the Dynamics of DNA and RNA Buckling. Biophys. J. 118, 1514-1516, https://doi.org/10.1016/j.bpj.2020.02.021

2018

55. F. Kriegel, C. Matek, T. Drsata, K. Kulenkampff, S. Tschirpke, M. Zacharias, F. Lankas, J. Lipfert (2018): The temperature dependence of the helical twist of DNA. Nucleic Acids Res. 46, 7998-8009, https://doi.org/10.1093/nar/gky599
 

2017

54. T. Drsata, K. Reblova, I. Besseova, J. Sponer, F. Lankas (2017): rRNA C-loops: Mechanical properties of a recurrent structural motif. J. Chem. Theory Comput. 13, 3359-3371
53. E. Bignon, T. Drsata, C. Morell, F. Lankas, E. Dumont (2017): Interstrand cross-linking implies contrasting structural consequences for DNA: Insights from molecular dynamics. Nucleic Acids Res. 45, 2188-2195
52. M. Zgarbova, P. Jurecka, F. Lankas, T. E. Cheatham III, J. Sponer, M. Otyepka (2017): Influence of BII backbone substates on DNA twist: A unified view and comparison of simulation and experiment for all 136 distinct tetranucleotide sequences. J. Chem. Inf. Model. 57, 275-287
 

2016

51. P. D. Dans, L. Danilane, I. Ivani, T. Drsata, F. Lankas, A. Hospital, J. Walther, R. I. Pujagut, F. Battistini, J. L. Gelpi, R. Lavery, M. Orozco (2016): Long-timescale dynamics of the Drew-Dickerson dodecamer. Nucleic Acids Res. 44, 4052-4066
50. T. Drsata, M. Zgarbova, P. Jurecka, J. Sponer, F. Lankas (2016): On the use of molecular dynamics simulations for probing allostery through DNA. Biophys. J. 110, 874-876
 

2015

49. K. Liebl, T. Drsata, F. Lankas, J. Lipfert, M. Zacharias (2015): Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis. Nucleic Acids Res. 43, 10143-10156
48. T. Drsata, F. Lankas (2015): Multiscale modelling of DNA mechanics. J. Phys. Condens. Matter 27, 323102
47. M. Kara, T. Drsata, F. Lankas, M. Zacharias (2015): Effect of O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations. Biopolymers 103, 23-32
46. E. Dumont, T. Drsata, C.F. Guerra, F. Lankas (2015): Insights into the structure of intrastrand cross-link DNA lesion-containing oligonucleotides: G[8-5m]T and G[8-5]C from molecular dynamics simulations. Biochemistry 54, 1259-1267
 

2014

45. T. Drsata, M. Zgarbova, N. Spackova, P. Jurecka, J. Sponer, F. Lankas (2014): Mechanical model of DNA allostery. J. Phys. Chem. Lett. 5, 3831-3835
44. M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T.E. Cheatham III, P.D. Dans, B. Jayaram, F. Lankas, C. Laughton, J. Mitchell, R. Osman, M. Orozco, A. Perez, D. Petkeviciute, N. Spackova, J. Sponer, K. Zakrzewska, R. Lavery (2014): µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res. 42, 12272-12283
43. M. Zgarbova, M. Otyepka, J. Sponer, F. Lankas, P. Jurecka (2014): Base pair fraying in molecular dynamics simulations of DNA and RNA.  J. Chem. Theory Comput. 10, 3177-3189
42. T. Drsata, N. Spackova, P. Jurecka, M. Zgarbova, J. Sponer, F. Lankas (2014): Mechanical properties of symmetric and asymmetric DNA A-tracts: Implications for looping and nucleosome positioning. Nucleic Acids Res 42, 7383-7394
 

2013

41. C. Patel, T. Drsata, F. Lankas, E. Dumont (2013): Structure, dynamics, and interactions of a C4’-oxidized abasic site in DNA: A concomitant strand scission reverses affinities. Biochemistry 52, 8115-8125
40. T. Dršata, M. Kara, M. Zacharias, F. Lankaš (2013): Effect of 8-oxoguanine on DNA structure and deformability. J. Phys. Chem. B 117, 11617-11622
39. T. Dršata, F. Lankaš (2013): Theoretical models of DNA flexibility. WIREs Comput. Mol. Sci. 3, 355-363
38. T. Dršata, A. Pérez, M. Orozco, A. V. Morozov, J. Šponer, F. Lankaš (2013): Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J. Chem. Theory Comput. 9, 707-721
 

2012

37. F. Lankaš (2012): Modelling nucleic acid structure and flexibility: From atomic to mesoscopic scale. In: Innovations in Biomolecular Modeling and Simulations, vol. 2, pp.3-32. Tamar Schlick, ed. Royal Society of Chemistry, London
36. T. Zelený, M. Ruckenbauer, A. J. A. Aquino, T. Muller, F. Lankaš, T. Dršata, W. L. Hase, D. Nachtigallova, H. Lischka (2012): Strikingly different effects of hydrogen bonding on the photodynamics of individual nucleobases in DNA: Comparison of guanine and cytosine. J. Am. Chem. Soc. 134, 13662-13669
35. K. Réblová, J. Šponer, F. Lankaš (2012): Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res. 40, 6290-6303
34. P. Banáš, A. Mládek, M. Otyepka, M. Zgarbová, P. Jurečka, D. Svozil, F. Lankaš, J. Šponer (2012): Can we accurately describe the structure of adenine tracts in B-DNA? Reference quantum-chemical computations reveal overstabilization of stacking by molecular mechanics. J. Chem. Theory Comput. 8, 2448-2460
33. M. Kabeláč, O. Kroutil, M. Předota, F. Lankaš, M. Šíp (2012): Influence of a charged graphene surface on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study. Phys. Chem. Chem. Phys. 14, 4217-4229
 

2011

32. P. Sklenovský, P. Florová, P. Banáš, K. Réblová, F. Lankaš, M. Otyepka, J. Šponer (2011): Understanding RNA flexibility using explicit solvent simulations: The ribosomal and group I intron reverse kink-turn motifs. J. Chem. Theory Comput. 7, 2963-2980
 

2010

31. F. Lankaš, N. Špačková, M. Moakher, P. Enkhbayar, J. Šponer (2010): A measure of bending in nucleic acids structures applied to A-tract DNA .Nucleic Acids Res. 38, 3414-3422
30. M. Kabelac, F. Lankas, F. Zimandl, T. Fessl (2010): Binding of QSY 21 Nonfluorescent quencher to DNA: Structure and Dynamics. International Conference on Networking and Information Technology, 516-520
29. R. Lavery, K. Zakrzewska, D. Beveridge, T.C. Bishop, D.A. Case, T.E. Cheatham III, S. Dixit, B. Jayaram, F. Lankaš, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Špačková, J. Šponer (2010): A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res. 38, 299-313
28. M. Kabeláč, F. Zimandl, T. Fessl, Z. Chval, F. Lankaš (2010): A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics. Phys. Chem. Chem. Phys. 12, 9677-9684
 

2009

27. F. Lankaš, O.Gonzalez, L.M. Heffler, G. Stoll, M. Moakher, J.H. Maddocks (2009): On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations. Phys. Chem. Chem. Phys. 11, 10565-10588
 

2008

26. A Perez, F Lankas, FJ Luque, M Orozco (2008): Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res. 36, 2379-2394
25. I. Horenko, E. Dittmer, F. Lankas, J.H. Maddocks, Ph. Metzner, Ch. Schuette (2008): Macroscopic dynamics of complex metastable systems – theory, algorithms, and application to B-DNA. SIAM J. Applied Dynamical Systems 7, 532-560
 

2007

24. K. Reblova, F. Lankas, J. Sponer (2007): Study of structure, dynamics and local elasticity of 16S rRNA helix 44 using molecular dynamics methods. J. Biomol. Struct. Dyn. 24, 635-636
23. T. Lionnet, F. Lankas (2007): Sequence-dependent twist-stretch coupling in DNA. Biophys. J. 92, L30-L32
 

2006

22. F. Lankas, R. Lavery, J.H. Maddocks (2006): Kinking occurs during molecular dynamics simulations of small DNA minicircles. Includes cover graphics. Structure 14, 1527-1534
21. F. Aumann, F. Lankas, M. Caudron, J. Langowski (2006): Monte Carlo Simulation of Chromatin Stretching. Phys. Rev. E 73, 041927
20. K. Reblova, F. Lankas, F. Razga, M.V. Krasovska, J. Koca, J. Sponer (2006): Structure, dynamics and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82, 504-520
19. F. Lankas (2006): Inferring shape and harmonic deformability of nucleic acids from atomistic molecular dynamics. In: Computational studies of RNA and DNA, pp. 559-577. J. Sponer and F. Lankas, eds. Springer.
 

2005

18. S.B. Dixit, D.L. Beveridge, D.A. Case, T.E. Cheatham III, E. Giudice, F. Lankas, R. Lavery, J.H. Maddocks, R. Osman, H. Sklenar, K. Thayer, P. Varnai (2005): Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II. Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J. 89, 3721-3740
17. F. Barone, F. Lankas, N. Spackova, J. Sponer, P. Karran, M. Bignami, F. Mazzei (2005): Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence. Biophys. Chem. 118, 31-41
16. F. Aumann, F. Lankas, M. Caudron, J. Langowski (2005): Chromatin flexibility simulated by a Monte Carlo model. Eur. Biophys. J. 34, 732
 

2004

15. D.L. Beveridge, G. Barreiro, K.S. Byun, D.A. Case, T.E. Cheatham III, S.B. Dixit, E. Giudice, F. Lankas, R. Lavery, J.H. Maddocks, R. Osman, E. Seibert, H. Sklenar, G. Stoll, K.M. Thayer, P. Varnai, M.A. Young (2004): Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps. Biophys. J. 87, 3799-3813
14. A. Perez, A. Noy, F. Lankas, F.J. Luque, M. Orozco (2004): The relative flexibility od B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res. 32, 6144-6151
13. A. Noy, A. Perez, F. Lankas, F.J. Luque, M. Orozco (2004): Relative Flexibility of DNA and RNA: a Molecular Dynamics Study. J. Mol. Biol. 343, 627-638
12. F. Lankas (2004): DNA Sequence-Dependent Deformability – Insights from Computer Simulations. Biopolymers 73, 327-339
11. F. Lankas, J. Sponer, J. Langowski, T.E. Cheatham III (2004): DNA Deformability at the Base Pair Level. J. Am. Chem. Soc. 126, 4124-4125
 

2003

10. F. Lankas, J. Sponer, J. Langowski, T.E. Cheatham III (2003): DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations. Biophys. J. 85, 2872-2883
9. F. Lankas, J. Sponer, T.E. Cheatham III, J. Langowski (2003): Multiscale modeling of DNA deformability. Biophys. J. 84 143A-143A, Part 2 Suppl. S
8. N. Spackova, T.E. Cheatham III, F. Ryjacek, F. Lankas, L.V. Meervelt, P. Hobza, J. Sponer (2003): Molecular Dynamics Simulations and Thermodynamics Analysis of DNA-Drug Complexes. Minor Groove Binding between 4’,6-Diamino-2-phenylindole and DNA Duplexes in Solution. J. Am. Chem. Soc. 125, 1759-1769
 

2002

7. F. Lankas, T.E. Cheatham III, N. Spackova, P. Hobza, J. Langowski, J. Sponer (2002): Critical Effect of the N2 Amino Group on Structure, Dynamics, and Elasticity of DNA Polypurine Tracts. Biophys. J. 82, 2592-2609
 

2001

6. F. Lankas, J. Sponer, P. Hobza, J. Langowski (2001): Global and local deformability of DNA oligonucleotides. J. Biomol. Struct. Dyn. 18, 993-994
 

2000

5. F. Lankas, J. Sponer, P. Hobza, J. Langowski (2000): Elasticity of DNA: Insights from molecular dynamics simulations. Eur. Biophys. J. 29, 252
4. F. Lankas, J. Sponer, P. Hobza, J. Langowski (2000): Sequence-dependent Elastic Properties of DNA. J. Mol. Biol. 299, 695-709
 

Dřívější publikace

3. F. Lankas (1997): Thermodynamic description of condensation waves. Thesis. Institute of Thermomechanics, Czech Academy of Sciences, Prague.
2. F. Marsik, J. Blaha, F. Lankas (1996): Nucleation and condensation rate measurement by condensation wave. In: Nucleation and Atmospheric Aerosols, Kulmala M and Wagner P, eds. Pergamon.
1. F. Lankas (1992): A 2D model of silicon oxidation in the presence of electric and stress fields. Acta Technica CSAV 37, 695-704