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Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
It is acknowledged that co-evolutionary nucleotide-nucleotide interactions are essential for RNA structures and functions. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
We study the binding of plant hormone IAA on its receptor TIR1 introducing a novel computational method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes.…
Dynamic models of signaling networks allow the formulation of hypotheses on the topology and kinetic rate laws characterizing a given molecular network, in-depth exploration and confrontation with kinetic biological data. Despite its…
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential…
Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…
We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…