The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

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

Background Molecular dynamics has emerged as an important research methodology
covering systems to the level of millions of atoms. However, insufficient sampling often limits …

Recent advances in hardware and software have enabled increasingly long molecular
dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of …

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

Structure-based and physics-based coarse-grained molecular force fields have become
attractive approaches to gain mechanistic insight into the function of large biomolecular …

Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …

GENESIS (Generalized‐Ensemble Simulation System) is a new software package for
molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called …

To accurately predict protein conformations in atomic detail, a computational method must
be capable of sampling models sufficiently close to the native structure. All-atom sampling is …

Free energy calculations are central to understanding the structure, dynamics and function
of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded …