Over the years, various computational methodologies have been developed to understand and quantify receptor-ligand interactions. Protein-ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when ...

Papain-like protease is a SARSCOV-2 that functions for ubiquitination in host cells. Caffeine compounds have been widely reported to antioxidant, anti-inflammatory, antidiabetic, and antiobesity activities. However, hexose malic acid coffee rind as potential inhibitors of the papain-like SARSCOV2 not reported. This study investigated PLPro inhibitor agents inhibiting ubiquitination. In silico s...

Understanding the physical attributes of protein-ligand interfaces, the source of most biological activity, is a fundamental problem in biophysics. Knowing the characteristic features of interfaces also enables the design of molecules with potent and selective interactions. Prediction of native protein-ligand interactions has traditionally focused on the development of physics-based potential e...

In keeping with the goals of our laboratory, efforts in this thesis are directed towards improving our understanding, and therefore our ability to calculate, the energetics of protein-ligand interactions. Electrostatic contributions to protein-ligand binding events are poorly understood, and underrepresented in data sets used to parameterize the energetics of protein unfolding and binding. Ther...

Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the modern drug discovery pipeline as it mitigates cost, time, and resources required to screen novel therapeutics. Deep Neural Networks (DNN) have recently shown excellent performance PLI prediction. However, highly dependent on protein ligand features utilized for DNN model. Moreover, current models, decipher...

background: protein-protein interactions do not provide any direct information re­garding the domains within the proteins that mediate the interactions. the majority of proteins are multi domain proteins and the interaction between them is often defined by the pairs of their domains. most of the former studies focus only on interacting do­main pairs. however they do not consider the interaction...

Protein-protein and protein-ligand interactions are ubiquitous in a biological cell. Here, we report a comprehensive study of the distribution of protein-ligand interaction sites, namely ligand-binding pockets, around protein-protein interfaces where protein-protein interactions occur. We inspected a representative set of 1,611 representative protein-protein complexes and identified pockets wit...