The phenomenon of molecular binding, where two molecules, referred to as a receptor and ligand, bind together form ligand-receptor complex, is ubiquitous in biology essential for the accurate functioning all life-sustaining processes. probability single forming complex with any one L surrounding ligand molecules at thermal equilibrium can be derived from partition function obtained Gibbs-Boltzm...

Cell adhesion on a supported lipid bilayer (SLB) functionalized with ligand proteins is widely-used cell-mimetic model for the study of trans receptor-ligand interaction that mediates adhesion, and has been shown to play an important role in unravelling molecular players cell adhesion. Experimental studies such cell-SLB systems often assume there no cis interactions between ligands. An question...

long-term potentiation (ltp) is a process that certain types of synaptic stimulation lead to a long-lasting enhancement in the strength of synaptic transmission. studies in recent years indicate the importance of molecular pathways in the development of memory and learning. tropomyosin receptor kinase b (trkb) is a member of the neurotrophin receptor tyrosine kinase family, that its ligand is b...

Abstract Herein we computationally explore the modulation of release kinetics an encapsulated guest molecule from cucurbit[7]uril ( CB7 ) cavity by ligands binding to host portal. We uncovered a correlation between ligand-binding affinity with and residence time, allowing us rapidly predict through straightforward energy minimization calculations. These high-throughput predictions in turn enabl...

The identification of ligand-binding sites is often the starting point for protein function annotation and structure-based drug design. Many computational methods for the prediction of ligand-binding sites have been developed in recent decades. Here we present a consensus method metaPocket, in which the predicted sites from four methods: LIGSITE(cs), PASS, Q-SiteFinder, and SURFNET are combined...

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the ...

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...