Binding affinity is a fundamental parameter in drug design, describing the strength of the
interaction between a molecule and its target protein. Accurately predicting binding affinity is …

Abstract Structure-based virtual screening is currently an established tool in drug lead
discovery projects. Although in the last years the field saw an impressive progress in terms …

Background Molecular docking methods are commonly used for predicting binding modes
and energies of ligands to proteins. For accurate complex geometry and binding energy …

In modeling ligand–protein interactions, the representation and role of water are of great
importance. We introduce a force field and hydration docking method that enables the …

Semi-empirical (SE) methods are derived from Hartree–Fock (HF) or Density Functional
Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are …

Quantum mechanical (QM) methods are becoming popular in computational drug design
and development mainly because high accuracy is required to estimate (relative) binding …

Molecular docking, which is the indispensable emphasis in predicting binding conformations
and energies of ligands to receptors, constructs the high-throughput virtual screening …

Predicting inhibitor potency is critical in drug design and development, yet it has remained
one of computational biology's biggest unresolved challenges. Here, we show that in the …

The p53 protein, also called guardian of the genome, plays a critical role in the cell cycle
regulation and apoptosis. This protein is frequently inactivated in several types of human …

A novel coronavirus (SARS-CoV-2) identified in Wuhan state of China in 2019 is the
causative agent of deadly disease COVID-19. It has spread across the globe (more than 210 …