List of works by Daniel Svozil

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

scientific article published on 18 October 2017

A DNA structural alphabet provides new insight into DNA flexibility

scientific article

Ab initio electronic structure of thymine anions

scientific article published in March 2005

Automatic workflow for the classification of local DNA conformations

scientific article

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

scientific article published on 29 April 2009

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

article by Arnošt Mládek et al published 2013 in Physical Chemistry Chemical Physics

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

scientific article published on 08 February 2022

Bioinformatic analysis of the protein/DNA interface.

scientific article published on 11 December 2013

Cluster Model for the Ionic Product of Water: Accuracy and Limitations of Common Density Functional Methods

article

Comment on "The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability".

scientific article published on 15 March 2018

Comment on “Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings”

scientific article published on 11 July 2012

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?

scientific article

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

article by Arnošt Mládek et al published 14 December 2010 in Journal of Chemical Theory and Computation

DNA conformations and their sequence preferences.

scientific article published on 13 May 2008

Efficient RNA pairwise structure comparison by SETTER method

scientific article

Electron Binding to Nucleic Acid Bases. Experimental and Theoretical Studies. A Review

article

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

scientific article

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

scientific article published on 30 July 2019

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

scientific article published in 2021

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

scientific article

InCHlib – interactive cluster heatmap for web applications

scientific article (publication date: December 2014)

Molpher: a software framework for systematic chemical space exploration

scientific article

MultiSETTER: web server for multiple RNA structure comparison

scientific article published on 12 August 2015

Multiple 3D RNA Structure Superposition Using Neighbor Joining

scientific article published on May 2015

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

scientific article

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

scientific article

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

scientific article published on 29 May 2020

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

scientific article published on 12 February 2010

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

scientific article (publication date: June 2007)

SETTER: web server for RNA structure comparison

scientific article

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

scientific article published on 16 October 2012

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

scientific article published in 2012

Valence- and dipole-bound anions of the thymine-water complex: ab initio characterization of the potential energy surfaces

scientific article published in March 2006

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