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Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using $\beta$-lactoglobulin fibrils as a model, that semiflexible…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
The formation of amyloid fibrils comprising amyloid $\beta$ (A$\beta$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$\beta$ structure at the fibril end using the density…
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neurotoxic than the end product, namely, the amyloid fibrils. In…
We review recent molecular dynamics simulations of thermally activated undulations and defects in the lamellar $L_\alpha$ phase of a binary amphiphile-solvent mixture, using an idealized molecular coarse-grained model: Solvent particles are…
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is…
We present a density-functional theory trend study addressing the binding of the trans-cis conformational switch azobenzene (C6H5-N=N-C6H5) at three coinage metal surfaces. From the reported detailed energetic, geometric, and electronic…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
Amyloid fibers are aggregates of proteins. They are built out of a peptide called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the…
Functionalization of photocatalytic metal oxide nanoparticles of TiO2, ZnO, WO3 and CuO with amine-terminated (oleylamine) and thiol-terminated (1-dodecanethiol) alkyl chained ligands was studied under ambient conditions. A high selectivity…
By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. This study highlights the important…
We present magnetic, thermodynamic, dielectric and structural investigations on the aluminoborate Ni${_2}$AlBO${_5}$, belonging to the ludwigite family. Room temperature structural refinement suggests that the system crystallizes in the…
We have carried out a detailed study of the chemical bonding for two room-temperature stable platinum silicide phases, tetragonal alpha-Pt_2Si and orthorhombic PtSi. An analysis of the valence electronic charge density reveals surprising…
In this work 2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate (CMA2OEM) molecule has been characterized theoretically. First, the potential energy surface has been calculated to find the lowest energy state of the molecule. After the most…
Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…
Recent advancements in protein docking site prediction have highlighted the limitations of traditional rigid docking algorithms, like PIPER, which often neglect critical stochastic elements such as solvent-induced fluctuations. These…
Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Ab) (1 42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid…