The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …

PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐
dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron …

Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …

Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …

Most biomolecular modeling energy functions for structure prediction, sequence design, and
molecular docking have been parametrized using existing macromolecular structural data; …

Innate immunity driven by pattern recognition receptor (PRR) protects the host from invading
pathogens. Aquatic animals like fish where the adaptive immunity is poorly developed …

Docking is now routine in virtual screening or lead optimization for drug screening and
design. The number of papers related to docking has dramatically increased over the past …

The protein-folding problem was first posed about one half-century ago. The term refers to
three broad questions:(i) What is the physical code by which an amino acid sequence …

The re-kindled fascination in machine learning (ML), observed over the last few decades,
has also percolated into natural sciences and engineering. ML algorithms are now used in …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …