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RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
Summary: We introduce RBPBind, a web-based tool for the quantitative prediction of RNA-protein interactions. Given a user-specified RNA and a protein selected from a set of several common RNA-binding proteins, RBPBind computes the binding…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…
Protein-protein and protein nucleic acid interactions are vitally important for a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have…
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…