相关论文: An elastic-network based local molecular field ana…
Zinc-fingers, which widely exist in eukaryotic cell and play crucial roles in life processes, depend on the binding of zinc ion for their proper folding. To computationally study the zinc coupled folding of the zinc-fingers, charge transfer…
The zinc finger structure where a Zn2+ ion binds to 4 cysteine or histidine amino acids in a tetrahedral structure is very common motif of nucleic acid binding proteins. The corresponding interaction model is present in 3% of the genes of…
The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
We studied acetylhistidine (AcH), bare or microsolvated with a zinc cation by simulations in isolation. First, a global search for minima of the potential energy surface combining both, empirical and first-principles methods, is performed…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
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…
The binding of small metal ions to complex macromolecular structures is typically dominated by strong local interactions of the ion with its nearest ligands. For this reason, it is often possible to understand the microscopic origin of ion…
A fully atomistic modelling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and it a posteriori analysis. This difficulty can be…
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate…
Choice of appropriate force field is one of the main concerns of any atomistic simulation that needs to be seriously considered in order to yield reliable results. Since, investigations on mechanical behavior of materials at micro/nanoscale…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Magnetic properties of metals are investigated through electronic structure calculations based on the recently-proposed magnetic-field-containing relativistic tight-binding approximation (MFRTB) method [Phys. Rev. B \textbf{91}, 075122…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
The major histocompatibility complex (MHC) molecules, which bind peptides for presentation on the cell surface, play an important role in cell-mediated immunity. In light of developing databases and technologies over the years, significant…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…