12 Result(s)
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Article
Special issue: Multiscale simulations of DNA from electrons to nucleosomes
This editorial for Volume 16, Issue 3 of Biophysical Reviews highlights the three-dimensional structural and dynamic information encoded in DNA sequences and introduces the topics covered in this special issue of...
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Article
Open AccessMD-DATA: the legacy of the ABC Consortium
The ABC Consortium has been generating nucleic-acids MD trajectories for more than 20 years. This brief comment highlights the importance of this data for the field, which triggered a number of critical studie...
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Article
Molecular strip** underpins derepression of a toxin–antitoxin system
Transcription factors control gene expression; among these, transcriptional repressors must liberate the promoter for derepression to occur. Toxin–antitoxin (TA) modules are bacterial elements that autoregulat...
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Article
An open call for contributions to a special issue of Biophysical Reviews focused on multiscale simulations of DNA from electrons to nucleosomes
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Article
Deciphering the mechanical code of the genome and epigenome
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (tha...
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Article
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution
The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes p...
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Article
Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and struc...
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Article
A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids
The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. This polyelectrolyte structure decouples information content (base sequence) from bulk p...
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Article
Visualizing phosphodiester-bond hydrolysis by an endonuclease
Different catalytic steps of endonuclease I-DmoI are captured crystallographically to allow direct observation of the generation of a DNA double-strand break. A third metal ion enters the active site and has a...
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Article
Open AccessBioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools i...
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Article
Open AccessComparison of molecular dynamics and superfamily spaces of protein domain deformation
It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential...
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Chapter
On the Use of SCRF Methods in Drug Design Studies
Self consistent reaction field (SCRF) methods have been largely used to examine solvent effects in chemical interactions. These methods’ are designed to determine solvation free energy, which is the reversible...
