Publications

This section contains a list of works published by the members of the Cheminformatics research group. The publications of individual members can be found under  their ORCID records.

2021

42. Wilm A, Norinder U, Agea MI, de Bruyn Kops C, Stork C, Kühnl J, Kirchmair J. Skin Doctor CP: Conformal Prediction of the Skin Sensitization Potential of Small Organic Molecules. Chem Res Toxicol. 2021 Feb 15;34(2):330-344. DOI: 10.1021/acs.chemrestox.0c00253

41. de Bruyn Kops C, Šícho M, Mazzolari A, Kirchmair J. GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. Chem Res Toxicol. 2021 Feb 15;34(2):286-299. DOI: 10.1021/acs.chemrestox.0c00224

40. Čmelo I, Voršilák M, Svozil D. Profiling and analysis of chemical compounds using pointwise mutual information. J Cheminform. 2021 Jan 10;13(1):3. DOI: 10.1186/s13321-020-00483-y

2020

39. Prihoda D, Maritz JM, Klempir O, Dzamba D, Woelk CH, Hazuda DJ, Bitton DA, Hannigan GD. The application potential of machine learning and genomics for understanding natural product diversity, chemistry, and therapeutic translatability. Nat Prod Rep. 2020 Nov 27. DOI: 10.1039/d0np00055h

38. Jurásek B., Čmelo I., Svoboda J. Čejka J., Svozil D., Kuchař M. New psychoactive substances on dark web markets: from deal solicitation to forensic analysis of purchased substances. Drug  Testing and Analysis 13 (1) 156-168 2020. DOI: 10.1002/dta.2901

37. Jurásek B., Bartůněk V., Huber Š., Fagan P., Setnička V., Králík F., Dehaen W., Svozil D., Kuchař M. Can X-Ray Powder Diffraction Be a Suitable Forensic Method for Illicit Drug Identification? Frontiers in Chemistry 8:499 2020. DOI: 10.3389/fchem.2020.00499

36. Cortés-Ciriano I., Škuta C., Bender A., Svozil D. QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. Journal of Cheminformatics 12:41 2020. DOI: 10.1186/s13321-020-00444-5

35. Škuta C., Cortés-Ciriano I., Dehaen W., Kříž P., van Westen G. J. P., Tetko I. V., Bender A., Svozil D. QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. Journal of Cheminformatics 12:39 2020. DOI: 10.1186/s13321-020-00443-6

34. Voršilák M., Kolář M., Čmelo I., Svozil D. SYBA: Bayesian estimation of synthetic accessibility of organic compounds. Journal of Cheminformatics 12:35 2020. DOI: 10.1186/s13321-020-00439-2

33. Stork C., Embruch B.,Šícho M., de Bruyn Kops C., Chen Y., Svozil D., Kirchmair J. NERDD: A web portal providing access to in silico tools for drug discovery. Bioinformatics 36 (4) 1291-1292 2020. DOI: 10.1093/bioinformatics/btz695

2019

32. Hannigan GD, Prihoda D, Palicka A, Soukup J, Klempir O, Rampula L, Durcak J, Wurst M, Kotowski J, Chang D, Wang R, Piizzi G, Temesi G, Hazuda DJ, Woelk CH, Bitton DA. A deep learning genome-mining strategy for biosynthetic gene cluster prediction. Nucleic Acids Res. 2019 Oct 10;47(18):e110. DOI: 10.1093/nar/gkz654

31. 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 Modelling 59 (8) 3400-3412 2019. DOI: 10.1021/acs.jcim.9b00376

30. de Bruyn Kops C., Stork C., Šícho M., Kochev N., Svozil D., Jeliazkova N., Kirchmair J. GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism. Frontiers in Chemistry 7:402 2019. DOI: 10.3389/fchem.2019.00402

29. Stork C, Chen Y, Šícho M, Kirchmair J. Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. J Chem Inf Model. 2019 Mar 25;59(3):1030-1043. DOI: 10.1021/acs.jcim.8b00677

2018

28. Voršilák M., Svozil D., Comment on "The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability". Journal of Cheminformatics 10:13 2018. DOI: 10.1186/s13321-018-0267-x

27. Schneider B., Božíková P., Nečasová I., Čech P.,  Svozil D., Černý J., A DNA structural alphabet provides new insight into DNA flexibility. Acta Cryst. D 74 52-64 2018. DOI: 10.1107/S2059798318000050

2017

• In November 2017, a special issue of Chemické listy on computer aided drug design was published. The authors of ten articles come from our department and from the Institute of Molecular Genetics of the ASCR. The articles are in the Czech language, here is a list of papers in which we participated as authors:
  
  1. Editorial: Svozil D., Bartůněk P., Computer Design of Drugs - Revaluated or Usable Helpers? Chemické listy 111 (11) 709-709 2017.
  2. Jirát J., Svozil D.,  Linear Representation of Chemical Structures. Chemické listy 111 (11) 710-715 2017.
  3. Novotný J., Svozil D., Characterization and Similarity Measurement of Molecules Using Molecular Descriptors? Chemické listy 111 (11) 716-723 2017.
  4. Čmelo I., Svozil D., Chemical Space. Chemické listy 111 (11) 724-730 2017.
  5. Svozil D., Virtual Screening. Chemické listy 111 (11) 738-746 2017.
  6. Škuta C., Svozil D., QSAR – Modelling of Quantitative Relations between Structure and Activity of Chemical Compounds. Chemické listy 111 (11) 747-753 2017.
  7. Šícho M., Svozil D., Molecular Docking as a Tool to Virtually Develop Drugs. Chemické listy 111 (11) 754-759 2017.
  8. Voršilák M., Svozil D., Estimation of Synthetic Accessibility during Computational Drug Design. Chemické listy 111 (11) 760-765 2017.

26. Schneider B., Božíková P., Čech P.,  Svozil D., Černý J., A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes 8 (10) 278 2017. DOI: 10.3390/genes8100278

25. Šícho M., de Bruyn Kops C., Stork C., Svozil D., Kirchmair J., FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity. Journal of Chemical Information and Modelling 57 (8) 1832-1846 2017. DOI: 10.1021/acs.jcim.7b00250

24. Škuta C., Popr M. Muller T., Jindřich J., Kahle M., Sedlák D., Svozil D., Bartůněk P., Probes & Drugs portal: an interactive, open data resource for chemical biology. Nature Methods 14 (8) 758-759 2017. DOI: 10.1038/nmeth.4365 

23. Voršilák M., Svozil D., Nonpher: computational method for design of hard-to-synthesize structures. Journal of Cheminformatics 9:20 2017. DOI: 10.1186/s13321-017-0206-2

2015

22. Čech P., Hoksza D., Svozil D.: MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinformatics 16 : 253 2015. DOI: 10.1186/s12859-015-0696-8

21. Hoksza D., Svozil D.: Multiple 3D RNA structure superposition using neighbor joining. IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics 12 (3): 520-530 2015. DOI: 10.1109/TCBB.2014.2351810

2014

20. Škuta C., Bartůněk P., Svozil D.: InCHlib - interactive cluster heatmap for web applications. Journal of Cheminformatics 6 : 44 2014. DOI: 10.1186/s13321-014-0044-4

19. Hoksza D., Škoda P., Voršilák M., Svozil D.: Molpher: a software framework for systematic chemical space exploration. Journal of Cheminformatics 6 : 7 2014. DOI: 10.1186/1758-2946-6-7

18. Schneider B., Černý J., Svozil D., Čech P., Gelly J.-P., de Brevern A. G.: Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Reasearch 42 (5): 3381-3394 2014. DOI: 10.1093/nar/gkt1273

2013

17. Hoksza D., Szepe P., Svozil D., MultiSETTER - Multiple RNA Structure Similarity Algorithm. 8th Brazilian Symposium on Bioinformatics (BSB) 2013, Recife, Brazil, ISBN 978-3-319-02623-7, pp. 59-70, Advances in Bioinformatics and Computational Biology, LNCS 8213, Springer. DOI: 10.1007/978-3-319-02624-4_6

16. Čech P., Kukal J., Černý J., Schneider B., Svozil D.: Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics 14: 205 2013. DOI: 10.1186/1471-2105-14-205

15. Mládek A., Krepl M., Svozil D., Čech P., Otyepka M., Banáš P., Zgarbová M., Jurečka P., Šponer J.: Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory. Physical Chemistry Chemical Physics 15 (19): 7295-7310 2013. DOI: 10.1039/C3CP44383C

14. Jirát J., Čech P., Znamenáček J., Šimek M., Škuta C., Vaněk T., Dibuszová E., Nic M., Svozil D..: Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic. Journal of Chemical Education 90 (3): 315-319 2013. DOI: 10.1021/ed3001446

2012

13. Šponer J., Mládek A., Šponer J. E., Svozil D., Zgarbová M., Banáš P., Jurečka P., Otyepka M., The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Physical Chemistry Chemical Physics 14 (44): 15257-15277 2012. DOI: 10.1039/c2cp41987d

12. Banáš P., Mládek A., Otyepka M., Zgarbová M., Jurečka P., Svozil D., Lankaš F., Šponer J., Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. Journal of Chemical Theory and Computation 8 (7): 2448-2460 2012. DOI: 10.1021/ct3001238

11. Šponer J., Morgado C. A., Svozil D.: Comment on "Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings". Journal of Physical Chemistry B 116 (28): 8331-8332. DOI: 10.1021/jp300659f

10. Morgado C. A., Svozil D., Turner D. H., Šponer J.: Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes. Physical Chemistry Chemical Physics 14 (36): 12580-12591 2012. DOI: 10.1039/C2CP40556C

9. Čech P., Svozil D., Hoksza D., SETTER: web server for RNA structure comparison. Nucleic Acids Research W1: W42-W48 2012. DOI: 10.1093/nar/gks560

8. Hoksza D., Svozil D., Efficient RNA pairwise structure comparison by SETTER method. Bioinformatics 28 (14): 1858-1864 2012. DOI: 10.1093/bioinformatics/bts301

2011

7. Čech P., Svozil D., mmView: a web-based viewer of the mmCIF format. BMC Research Notes 4:121 2011. DOI: 10.1186/1756-0500-4-121

6. Hoksza D., Svozil D., Exploration of Chemical Space by Molecular Morphing. IEEE International Conference on Bioinformatics & Bioengineering (BIBE) 2011, Taiwan, ISBN 978-0-7695-4391-8, pp. 201-208. DOI: 10.1109/BIBE.2011.38

5. Hoksza D., Svozil D., SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. 7th International Symposium on Bioinformatics Research and Applications (ISBRA) 2011, Central South University, China, ISBN 978-3-642-21259-8, pp. 37-49, LNBI 6674, Springer. DOI: 10.1007/978-3-642-21260-4_8

2010

4. Svozil D., Multilayer Neural Networks in Bioinformatics, in Artificial Intelligence and Congnitive Science II, V. Kvasnicka, J. Pospichal (Eds.), Publishing House of Slovak Technical University, Bratislava, 2010. Book chapter

3. Mládek A., Šponer J. E., Jurečka P., Banáš P., Otyepka M., Svozil D., Šponer J., Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. Journal of Chemical Theory and Computation 12 (6): 3817-3835 2010. DOI: 10.1021/ct1004593

2. Morgado C. A., Jurečka P., Svozil D., Hobza P., Šponer J., Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Physical Chemistry Chemical Physics 12 (14): 3522-3534 2010. DOI: 10.1039/b924461a

1. Svozil D., Hobza P., Šponer J., Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations? Journal of Physical Chemistry B 114 (2): 1191-1203 2010. DOI: 10.1021/jp910788e