Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of speci...

The Epstein-Barr virus determinant peptide EENLLDFVRF shows high immunogenicity when presented by HLA-B*4405 allotype. This fact is accompanied by a cis-trans isomerization of the Leu5-Asp6 peptide bond upon TCR binding of the pMHC complex. Molecular dynamics simulations of pMHC/TCR structures, with the EENLLDFVRF peptide in cis and trans conformations have been employed in order to examine the...

We review recent theoretical and algorithmic advances for the modeling of protein ligand binding free energies. We first describe a statistical mechanics theory of noncovalent association, with particular focus on deriving the fundamental formulas on which computational methods are based. The second part reviews the main computational models and algorithms in current use or development, pointin...

It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal-mode an...

Coronavirus 19 (COVID-19) is still a global health issue to date, SARS-CoV-2 novel coronavirus that responsible for this sickness. The receptor-binding domain of the virus associates with angiotensin-converting enzyme 2 (ACE-2) and allows enter human cells. Natural peptides such alpha-defensin are thought attach RBD prohibit it from engaging ACE-2. Molecular dynamics simulations using computati...

DNA sliding clamps are structurally conservative toroid-shape proteins that encircle and slide along DNA, serving as scaffold for other functional enzymes to act on DNA and ensuring the replication proccessivity, thereby, of fundamental biological significance across domains of life. Mechanistic details and related functional implications concerning clamp opening, interaction between clamp and ...