2019
47. 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 XX (X) YYYY-YYYY 2019. DOI: 10.1093/bioinformatics/btz695
46. 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
45. 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
2018
44. 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
43. 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
- V listopadu 2017 vyšlo zvláštní číslo Chemických listů věnované počítačovému návrhu léčiv. Autoři deseti článků pochází z našeho pracoviště a z Ústavu molekulární genetiky AV ČR. Články jsou v českém jazyce, zde je seznam příspěvků, na kterých jsme se autorsky podíleli:
- Úvodník: Svozil D., Bartůněk P., Computer Design of Drugs - Revaluated or Usable Helpers? Chemické listy 111 (11) 709-709 2017.
- Jirát J., Svozil D., Linear Representation of Chemical Structures. Chemické listy 111 (11) 710-715 2017.
- Novotný J., Svozil D., Characterization and Similarity Measurement of Molecules Using Molecular Descriptors? Chemické listy 111 (11) 716-723 2017.
- Čmelo I., Svozil D., Chemical Space. Chemické listy 111 (11) 724-730 2017.
- Svozil D., Virtual Screening. Chemické listy 111 (11) 738-746 2017.
- Škuta C., Svozil D., QSAR – Modelling of Quantitative Relations between Structure and Activity of Chemical Compounds. Chemické listy 111 (11) 747-753 2017.
- Šícho M., Svozil D., Molecular Docking as a Tool to Virtually Develop Drugs. Chemické listy 111 (11) 754-759 2017.
- Voršilák M., Svozil D., Estimation of Synthetic Accessibility during Computational Drug Design. Chemické listy 111 (11) 760-765 2017.
42. 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
41. 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
40. 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
39. 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
38. 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
37. 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
36. 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
35. 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
34. 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
33. 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
32. 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
31. 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
30. 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
29. 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
28. 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
27. 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
26. 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
25. 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
24. Hoksza D., Svozil D., Efficient RNA pairwise structure comparison by SETTER method. Bioinformatics 28 (14): 1858-1864 2012. DOI: 10.1093/bioinformatics/bts301
2011
23. 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
22. 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
21. 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
20. 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
19. 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
18. 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
17. 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
2009
16. Morgado C. A., Jurečka P., Svozil D., Hobza P., Šponer J., Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description. Journal of Chemical Theory and Computation 5 (6): 1524-1544 2009. DOI: 10.1021/ct9000125
2008
15. Banáš P., Rulíšek L., Hanošová V., Svozil D., Waltr N. G., Šponer J., Otyepka M., General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility. Journal of Physical Chemistry B 112 (35): 11177-11187 2008. DOI: 10.1021/jp802592z
14. Svozil D., Šponer J. E., Marchan I., Perez A., Cheatham T. E., Forti F., Luque F. J., Orozco M., Sponer J., Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. Journal of Physical Chemistry B 112 (27): 8188-8197 2008. DOI: 10.1021/jp801245h
13. Svozil D., Kalina J., Omelka M., Schneider B., DNA conformations and their sequence preferences. Nucleic Acids Research 36 (11): 3690-3706 2008. DOI: 10.1093/nar/gkn260
2007
12. Perez A., Marchan I., Svozil D., Šponer J., Cheatham T. E., Laughton C. A., Orozco M., Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophysical Journal 92 (11): 3817-3829 2007. DOI: 10.1529/biophysj.106.097782
2006
11. Griffiths M. L., Svozil D., Worsfold P. J., Evans E. H., The application of piecewise direct standardisation with variable selection to the correction of drift in inductively coupled atomic emission spectrometry. Journal Of Analytical Atomic Spectrometry 21 (10): 1045-1052 2006. DOI: 10.1039/B604728A
10. Svozil D., Jungwirth P., Cluster model for the ionic product of water: Accuracy and limitations of common density functional methods. Journal Of Physical Chemistry A 110 (29): 9194 - 9199 2006. DOI: 10.1021/jp0614648
9. Frigato T., Svozil D., Jungwirth P., Valence and dipole bound anions of the thymine-water complex: ab initio characterization of the potential energy surface. Journal Of Physical Chemistry A 110 (9): 2916-2923 2006. DOI: 10.1021/jp054090b
2005
8. Svozil D., Frigato T., Havlas Z., Jungwirth P., Ab initio electronic structure of thymine anions. Physical Chemistry Chemical Physics 7 (5): 840-845 2005. DOI: 10.1039/B415007D
2004
7. Svozil D., Jungwirth P., Havlas Z., Electron binding to nucleic acid bases. Experimental and theoretical studies. A review. Collection Of Czechoslovak Chemical Communications 69 (7): 1395-1428 2004. DOI: 10.1135/cccc20041395
2002
6. Griffiths M. L., Svozil D., Worsfold P. J., Denham S., Evans E. H., Variable reduction algorithm for atomic emission spectra: application to multivariate calibration and quantitative analysis of industrial samples. Journal Of Analytical Atomic Spectrometry 17 (8): 800-812 2002. DOI: 10.1039/B203239M
2000
5. Griffiths M. L., Svozil D., Worsfold P. J., Denham S., Evans E. H., Comparison of traditional and multivariate calibration techniques applied to complex matrices using inductively coupled plasma atomic emission spectroscopy. Journal Of Analytical Atomic Spectrometry 15 (8): 967-972 2000. DOI: 10.1039/B001582M
1997
4. Svozil D., Kvasnička V., Pospíchal J., Introduction to multi-layer feed-forward neural networks. Chemometrics And Intelligent Laboratory Systems 39 (1): 43-62 1997, DOI: 10.1016/S0169-7439(97)00061-0
3. Svozil D., Ševcik J. G., Kvasnička V, Neural network prediction of the solvatochromic polarity/polarizability parameter pi(H)(2). Journal Of Chemical Information And Computer Sciences 37 (2): 338-342 1997, DOI: 10.1021/ci960347e
1995
2. Svozil D., Pospíchal J., Kvasnička V., Neural-network prediction of C-13 NMR chemical-shifts of alkanes. Journal Of Chemical Information And Computer Sciences 35 (5): 924-928 1995, DOI: 10.1021/ci00027a021
1. Opekar F., Svozil D., Electric-resistance in a Nafion membrane exposed to air after a step change in the relative-humidity. Journal of Electroanalytical Chemistry 385 (2): 269-271 1995, DOI: 10.1016/0022-0728(95)03767-B