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Items: 1 to 20 of 31

1.

FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes.

Šícho M, Stork C, Mazzolari A, de Bruyn Kops C, Pedretti A, Testa B, Vistoli G, Svozil D, Kirchmair J.

J Chem Inf Model. 2019 Aug 13. doi: 10.1021/acs.jcim.9b00376. [Epub ahead of print]

PMID:
31361490
2.

GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism.

de Bruyn Kops C, Stork C, Šícho M, Kochev N, Svozil D, Jeliazkova N, Kirchmair J.

Front Chem. 2019 Jun 12;7:402. doi: 10.3389/fchem.2019.00402. eCollection 2019.

3.

A DNA structural alphabet provides new insight into DNA flexibility.

Schneider B, Boǽíková P, Nečasová I, Čech P, Svozil D, Černý J.

Acta Crystallogr D Struct Biol. 2018 Jan 1;74(Pt 1):52-64. doi: 10.1107/S2059798318000050. Epub 2018 Jan 1.

4.

Nonpher: computational method for design of hard-to-synthesize structures.

Voršilák M, Svozil D.

J Cheminform. 2017 Mar 20;9(1):20. doi: 10.1186/s13321-017-0206-2.

5.

A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle.

Schneider B, Božíková P, Čech P, Svozil D, Černý J.

Genes (Basel). 2017 Oct 18;8(10). pii: E278. doi: 10.3390/genes8100278.

6.

FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity.

Šícho M, de Bruyn Kops C, Stork C, Svozil D, Kirchmair J.

J Chem Inf Model. 2017 Aug 28;57(8):1832-1846. doi: 10.1021/acs.jcim.7b00250. Epub 2017 Aug 7.

7.

Probes &Drugs portal: an interactive, open data resource for chemical biology.

Skuta C, Popr M, Muller T, Jindrich J, Kahle M, Sedlak D, Svozil D, Bartunek P.

Nat Methods. 2017 Jul 28;14(8):759-760. doi: 10.1038/nmeth.4365. No abstract available.

PMID:
28753599
8.

Multiple 3D RNA Structure Superposition Using Neighbor Joining.

Hoksza D, Svozil D.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):520-30. doi: 10.1109/TCBB.2014.2351810.

PMID:
26357263
9.

MultiSETTER: web server for multiple RNA structure comparison.

Čech P, Hoksza D, Svozil D.

BMC Bioinformatics. 2015 Aug 12;16:253. doi: 10.1186/s12859-015-0696-8.

10.

InCHlib - interactive cluster heatmap for web applications.

Skuta C, Bartůněk P, Svozil D.

J Cheminform. 2014 Sep 17;6(1):44. eCollection 2014 Dec.

11.

Molpher: a software framework for systematic chemical space exploration.

Hoksza D, Skoda P, Voršilák M, Svozil D.

J Cheminform. 2014 Mar 21;6(1):7. doi: 10.1186/1758-2946-6-7.

12.

Bioinformatic analysis of the protein/DNA interface.

Schneider B, Cerný J, Svozil D, Cech P, Gelly JC, de Brevern AG.

Nucleic Acids Res. 2014 Mar;42(5):3381-94. doi: 10.1093/nar/gkt1273. Epub 2013 Dec 11.

13.

Automatic workflow for the classification of local DNA conformations.

Čech P, Kukal J, Černý J, Schneider B, Svozil D.

BMC Bioinformatics. 2013 Jun 25;14:205. doi: 10.1186/1471-2105-14-205.

14.

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.

Mládek A, Krepl M, Svozil D, Cech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Sponer J.

Phys Chem Chem Phys. 2013 May 21;15(19):7295-310. doi: 10.1039/c3cp44383c.

PMID:
23575975
15.

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.

Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M.

Phys Chem Chem Phys. 2012 Nov 28;14(44):15257-77. doi: 10.1039/c2cp41987d. Epub 2012 Oct 16. Review.

PMID:
23072945
16.

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics.

Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J.

J Chem Theory Comput. 2012 Jul 10;8(7):2448-60. doi: 10.1021/ct3001238. Epub 2012 Jun 6.

PMID:
26588974
17.

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes.

Morgado CA, Svozil D, Turner DH, Šponer J.

Phys Chem Chem Phys. 2012 Sep 28;14(36):12580-91. doi: 10.1039/c2cp40556c. Epub 2012 Jun 21.

PMID:
22722325
18.

SETTER: web server for RNA structure comparison.

Cech P, Svozil D, Hoksza D.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W42-8. doi: 10.1093/nar/gks560. Epub 2012 Jun 11.

19.

Comment on "Computational model for predicting experimental RNA and DNA nearest-neighbor free energy rankings".

Šponer J, Morgado CA, Svozil D.

J Phys Chem B. 2012 Jul 19;116(28):8331-2; author reply 8333-4. doi: 10.1021/jp300659f. Epub 2012 Jul 11. No abstract available.

PMID:
22686484
20.

Efficient RNA pairwise structure comparison by SETTER method.

Hoksza D, Svozil D.

Bioinformatics. 2012 Jul 15;28(14):1858-64. doi: 10.1093/bioinformatics/bts301. Epub 2012 May 18.

PMID:
22611129

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