Computational research plays an essential role in understanding, developing, and optimizing new scientific research methods, enhancing the research capabilities in any scientific or engineering discipline. The combination of significant advances in modeling methods and the exponential increase in available computational power means that computational modeling has a revolutionary impact on scientific research and discovery.

Biomedical simulations can provide insight into mechanisms at the molecular level, leading investigators in new directions. As a result, sub-specialties such as molecular modeling encompass a vast collection of computational techniques, including visualization, transition state modeling, ab initio (quantum mechanics), molecular docking, and molecular dynamics (MD). These methods are now standard tools used by theoretical/computational chemists and biologists for predicting the chemical structural properties of biomolecules.

This Methods Collection aims to highlight the latest computational tools for biophysical simulations and molecular modeling. The collection will cover but is not limited to the following:

·      Quantum mechanical simulations, e.g., ab initio, QM/MM, and transition state modeling.

·      Molecular dynamics (MD), coarse grain and all-atom simulations

·      Computer-aided drug discovery (CADD), protein-ligand, and protein-protein interactions