Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Monovalent ions play significant roles in various biological and material systems. Recently,
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …

Classical 3-point rigid water models are most widely used due to their computational
efficiency. Recently, we introduced a new approach to constructing classical rigid water …

Recently, molecular fingerprints extracted from three-dimensional (3D) structures using
advanced mathematics, such as algebraic topology, differential geometry, and graph theory …

This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …

Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP)
remain a challenge: widely used,“general purpose” water models tend to favor overly …

The SAMPL challenges focus on testing and driving progress of computational methods to
help guide pharmaceutical drug discovery. However, assessment of methods for predicting …

Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility
and its recognition by other macromolecules. Here we generate extensive atomic level …

The rationalization of non‐covalent binding trends is both of fundamental interest and
provides new design concepts for biomimetic molecular systems. Cucurbit [n] urils (CBn) are …