The function of a protein is dependent on whether and how it can interact with various ligands. Therefore, an accurate prediction of protein-ligand interactions is paramount to understanding proteins’ biological mechanisms and hence to the development of therapeutic agents. A ligand is most likely to bind in the largest pocket on the surface of the protein. Moreover, it requires that the pocket...

Understanding of protein-ligand interactions and its influences on protein stability is necessary in the research on all biological processes and correlative applications, for instance, the appropriate affinity ligand design for the purification of bio-drugs. In this study, computational methods were applied to identify binding site interaction details between trastuzumab and its natural recept...

A novel coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), enters into the host cells through an interaction between its surface spike protein (S-protein) and angiotensin-converting enzyme receptors, leading to disease 2019 (COVID-19). Using effective S-protein inhibitors may reduce virulence of virus. Molecular docking was performed evaluate binding affinity 97...

Recognition of functional partners is a pivotal factor in the regulation protein interactions. The areas direct contact between complementary molecules that interact according to Koshland’s "key - lock" scheme deserve special attention. relevance study this kind interactions obvious. In case simplest serine proteinases increased affinity enzyme certain area target ensured by synchronous interac...

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein- ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the st...

Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybr...

When studying protein-ligand interactions, many different factors can influence the behaviour of protein as well ligands. Molecular visualisation tools typically concentrate on movement single ligand molecules; however, viewing only one molecule merely provide a hint overall system. To tackle this issue, we do not focus local actions individual molecules but and their movement. Since simulation...