D. Svozil

发表

Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

J. Šponer, M. Orozco, T. Cheatham, 2007 .

Bioinformatic analysis of the protein/DNA interface

Daniel Svozil, Jean-Christophe Gelly, Jiří Černý, 2011, Nucleic acids research.

BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning

Danny A. Bitton, D. Svozil, A. Waight, 2021, bioRxiv.

An enumeration of natural products from microbial, marine and terrestrial sources

D. Svozil, F. Ntie‐Kang, 2020, Physical Sciences Reviews.

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Daniel Svozil, Charles A Laughton, Modesto Orozco, 2007, Biophysical journal.

Electric resistance in a Nafion® membrane exposed to air after a step change in the relative humidity

Daniel Svozil, D. Svozil, F. Opekar, 1995 .

Nucleic Acids Research

B. Schneider, M. Omelka, D. Svozil, 2010, Nucleic Acids Research.

The application of piecewise direct standardisation with variable selection to the correction of drift in inductively coupled atomic emission spectrometry

P. Worsfold, D. Svozil, E. Evans, 2006 .

Comparison of traditional and multivariate calibration techniques applied to complex matrices using inductively coupled plasma atomic emission spectroscopy

P. Worsfold, S. Denham, D. Svozil, 2000 .

Profiling and analysis of chemical compounds using pointwise mutual information

D. Svozil, I. Čmelo, M. Voršilák, 2020, Journal of Cheminformatics.

GenUI: Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation

D. Svozil, Xuhan Liu, G. V. Van westen, 2021 .

GenUI: Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation

D. Svozil, Xuhan Liu, G. V. Van westen, 2021 .

New psychoactive substances on dark web markets: from deal solicitation to forensic analysis of purchased substances.

D. Svozil, J. Svoboda, J. Čejka, 2020, Drug testing and analysis.

SYBA: Bayesian estimation of synthetic accessibility of organic compounds

D. Svozil, M. Kolář, I. Čmelo, 2020, Journal of Cheminformatics.

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

B. Schneider, D. Svozil, J. Černý, 2017, Genes.

Automatic workflow for the classification of local

Bohdan Schneider, Jaromír Kukal, Daniel Svozil, 2013 .

Automatic workflow for the classification of local DNA conformations

Bohdan Schneider, Petr Cech, Jaromir Kukal, 2013, BMC Bioinformatics.

DNA conformations and their sequence preferences

Daniel Svozil, Jan Kalina, Marek Omelka, 2008, Nucleic acids research.

Introduction to multi-layer feed-forward neural networks

Daniel Svozil, Jiri Pospichal, Vladimír Kvasnička, 1997 .

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

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Physical chemistry chemical physics : PCCP.

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

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Journal of chemical theory and computation.

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.

J. Šponer, M. Otyepka, P. Banáš, 2013, Physical chemistry chemical physics : PCCP.

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

Daniel Svozil, F. J. Luque, Modesto Orozco, 2008, The journal of physical chemistry. B.

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

D. Turner, J. Šponer, D. Svozil, 2012, Physical chemistry chemical physics : PCCP.

Conformational Energies of DNA Sugar-Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

J. Šponer, M. Otyepka, P. Banáš, 2010 .

NERDD: a web portal providing access to in silico tools for drug discovery

Daniel Svozil, Ya Chen, Johannes Kirchmair, 2019, Bioinform..

Novel D2/5-HT receptor modulators related to cariprazine with potential implication to schizophrenia treatment.

H. Stark, A. Bojarski, T. Petrásek, 2022, European journal of medicinal chemistry.

Ab initio electronic structure of thymine anions.

D. Svozil, P. Jungwirth, Z. Havlas, 2005, Physical chemistry chemical physics : PCCP.

Electron binding to nucleic acid bases. Experimental and theoretical studies. A review

D. Svozil, P. Jungwirth, Z. Havlas, 2004 .

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.

Daniel Svozil, Pavel Hobza, Petr Jurecka, 2010, Physical chemistry chemical physics : PCCP.

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.

J. Šponer, D. Svozil, P. Hobza, 2009, Journal of chemical theory and computation.

Trait divergence in river and reservoir populations of Australian smelt (Retropinna semoni)

D. Svozil, 2018 .

Morphological predictors of swimming speed performance in river and reservoir populations of Australian smelt Retropinna semoni.

D. Svozil, L. Baumgartner, C. Fulton, 2020, Journal of fish biology.

A DNA structural alphabet provides new insight into DNA flexibility

Bohdan Schneider, Daniel Svozil, Jiří Černý, 2018, Acta crystallographica. Section D, Structural biology.

QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction

Daniel Svozil, Andreas Bender, Isidro Cortés-Ciriano, 2020, Journal of Cheminformatics.

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

Daniel Svozil, Nina Jeliazkova, Johannes Kirchmair, 2019, Front. Chem..

Efficient RNA pairwise structure comparison by SETTER method

Daniel Svozil, David Hoksza, D. Svozil, 2012, Bioinform..

QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping

D. Svozil, C. Škuta, I. Cortés-Ciriano, 2020, Journal of Cheminformatics.

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

Daniel Svozil, Milan Voršilák, D. Svozil, 2017, Journal of Cheminformatics.

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

Daniel Svozil, Jindrich Jindrich, Ctibor Skuta, 2017, Nature Methods.

InCHlib – interactive cluster heatmap for web applications

Daniel Svozil, Ctibor Skuta, Petr Bartunek, 2014, Journal of Cheminformatics.

Neural Network Prediction of the Solvatochromic Polarity/Polarizability Parameter PiH2[S_EL2;quad]

Daniel Svozil, Vladimir Kvasnicka, Jirí G. K. Sevvík, 1997, J. Chem. Inf. Comput. Sci..

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.

J. Šponer, N. Walter, M. Otyepka, 2008, The journal of physical chemistry. B.

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics

Daniel Svozil, Martin Šícho, Xuhan Liu, 2021, Journal of Cheminformatics.

SETTER: web server for RNA structure comparison

Petr Cech, Daniel Svozil, David Hoksza, 2012, Nucleic Acids Res..

Variable reduction algorithm for atomic emission spectra: application to multivariate calibration and quantitative analysis of industrial samples

P. Worsfold, S. Denham, D. Svozil, 2002 .

Molpher: a software framework for systematic chemical space exploration

Daniel Svozil, David Hoksza, Petr Skoda, 2014, Journal of Cheminformatics.

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

Daniel Svozil, Johannes Kirchmair, Conrad Stork, 2017, J. Chem. Inf. Model..

Pharmacokinetic, pharmacodynamic, and behavioural studies of deschloroketamine in Wistar rats

L. Vyklický, W. Dehaen, D. Svozil, 2021, British journal of pharmacology.

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

Daniel Svozil, Alessandro Pedretti, Johannes Kirchmair, 2019, J. Chem. Inf. Model..

Can X-Ray Powder Diffraction Be a Suitable Forensic Method for Illicit Drug Identification?

W. Dehaen, D. Svozil, V. Setnička, 2020, Frontiers in Chemistry.

Macro-invertebrate species diversity as a potential universal measure of wetland ecosystem integrity in constructed wetlands in South East Melbourne

D. Svozil, S. Awal, 2010 .

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics

D. Svozil, M. Sicho, X. Liu, 2021, Journal of Cheminformatics.

Cluster model for the ionic product of water: accuracy and limitations of common density functional methods.

D. Svozil, P. Jungwirth, 2006, The journal of physical chemistry. A.

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?

J. Šponer, D. Svozil, P. Hobza, 2010, The journal of physical chemistry. B.

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

J. Šponer, D. Svozil, Claudio A. Morgado, 2012, The journal of physical chemistry. B.

mmView: a web-based viewer of the mmCIF format

Daniel Svozil, Petr Čech, D. Svozil, 2011, BMC Research Notes.

Activity-driven exploration of chemical space with morphing

Daniel Svozil, David Hoksza, Martin Sicho, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Multiple 3D RNA Structure Superposition Using Neighbor Joining

Daniel Svozil, David Hoksza, D. Svozil, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

MultiSETTER - Multiple RNA Structure Similarity Algorithm

Daniel Svozil, David Hoksza, Peter Szépe, 2013, BSB.