Antibodies are specialized proteins produced by our adaptive immune system to identify and neutralize specific molecules (antigens) of foreign objects, such as pathogenic microorganisms or infected cells. Due to their ...

Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few ...

Computing binding free energies has great implications in drug design. Using PELE technique, it has been shown that one can get quick and accurate estimations by means of a Markov state model3. We improved our methodology ...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes respiratory disease, but it can also affect other organs including the central nervous system. Several animal models have been developed to address different ...

We present a multistep protocol, combining Monte Carlo and molecular dynamics simulations, for the estimation of absolute binding free energies, one of the most significant challenges in computer-aided drug design. The ...

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing ...

Proteases are abundant in prokaryotic genomes (~10 per genome), but their recovery encounters expression problems, as only 1% can be produced at high levels; this value differs from that of similarly abundant esterases ...

The early stages of drug design rely on hit discovery programs, where initial possible inhibitors’ binding affinities are assessed when bound to their biological target. It is an expensive and time-consuming process, ...