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- JIŘÍ ČERNÝ
- 2009

We study the trajectory of a simple random walk on a d-regular graph with d ≥ 3 and locally tree-like structure as the number n of vertices grows. Examples of such graphs include random d-regular graphs and large girth expanders. For these graphs, we investigate percolative properties of the set of vertices not visited by the walk until time un, where u > 0… (More)

- Jirí Cerný, Augusto Teixeira
- Random Struct. Algorithms
- 2013

We consider the simple random walk on a random d-regular graph with n vertices, and investigate percolative properties of the set of vertices not visited by the walk until time un, where u > 0 is a fixed positive parameter. It was shown in [ ˇ CTW11] that this so-called vacant set exhibits a phase transition at u = u : there is a giant component if u < u… (More)

- Petr Jurecka, Jirí Cerný, Pavel Hobza, Dennis R. Salahub
- Journal of Computational Chemistry
- 2007

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable… (More)

- Pierrick Craveur, Agnel P. Joseph, +21 authors Alexandre G. de Brevern
- Front. Mol. Biosci.
- 2015

Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the… (More)

- Jiří Černý, Barbora Černá Bolfíková, James J. Valdés, Libor Grubhoffer, Daniel Růžek
- PloS one
- 2014

Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in… (More)

- Jǐrí Černý
- 2011

We consider a random walk among unbounded random conductances on the two-dimensional integer lattice. When the distribution of the conductances has an infinite expectation and a polynomial tail, we show that the scaling limit of this process is the fractional kinetics process. This extends the results of the paper [B ˇ C10] where a similar limit statement… (More)

- Bohdan Schneider, Jean-Christophe Gelly, Alexandre G. de Brevern, Jiří Černý
- Acta crystallographica. Section D, Biological…
- 2014

The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of… (More)

- Milan Kuchař, Lucie Vaňková, +9 authors Petr Malý
- Proteins
- 2014

Engineered combinatorial libraries derived from small protein scaffolds represent a powerful tool for generating novel binders with high affinity, required specificity and designed inhibitory function. This work was aimed to generate a collection of recombinant binders of human interleukin-23 receptor (IL-23R), which is a key element of proinflammatory… (More)

- Bohdan Schneider, Jiří Černý, Daniel Svozil, Petr Čech, Jean-Christophe Gelly, Alexandre G. de Brevern
- Nucleic acids research
- 2014

To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of… (More)

- Petr Cech, Jaromir Kukal, Jirí Cerný, Bohdan Schneider, Daniel Svozil
- BMC Bioinformatics
- 2012

A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with dinucleotide steps exhibiting a substantial flexibility in a sequence-dependent manner. An analysis of the conformational space of the DNA backbone and… (More)