The small-angle X-ray scattering (SAXS) methodology enables structural characterization of biological macromolecules in solution. However, because SAXS provides low-dimensional information, several potential structural configurations can reproduce the experimental scattering profile, which severely complicates the structural refinement process. Here, we present a bias-exchange metadynamics refi...

The use of beta solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their mechanical strengths, we can efficiently design the proteins for specific functions. We present a study of the mechanical properties of seven beta solenoid protein...

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from pr...

Telomere is a nucleoprotein complex that plays important role in stability and their maintenance and consists of random repeats of species specific motifs. In budding Saccharomyces cerevisiae, Repressor Activator Protein 1 (Rap1) is a sequence specific protein that involved in transcriptional regulation. Rap1 consist of three active domains like N-terminal BRCT-domain, DNA-binding domain and C-...

MOTIVATION Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. ...

Antimicrobial peptides (AMP) are a promising source of antibiotics with a broad spectrum activity against bacteria and low incidence of developing resistance. The mechanism by which an AMP executes its function depends on a set of computable physicochemical properties from the amino acid sequence. Peptides package was designed for allowing the quick and easy computation of ten structural charac...

We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the ...

Conductance measurements of the transmembrane porin protein OmpF as a function of pH and bath concentration have been made with both a microfabricated silicon substrate device and a commercially available polystyrene aperture. Ion transport through the channel was simulated in atomic detail: the measured current was compared with theoretically calculated current, using a Brownian Dynamics kerne...

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat. Traditional herbals and dietary plants with medicinal values have long antiviral history and, thus, are extensively studied in COVID-19 therapeutics development. Breadfruit (Artocarpus altilis) food crop rich nutrient composition. This study screened selected bre...