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 …

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

The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …

Intrinsically disordered proteins (IDPs) play crucial roles in cellular processes and hold
promise as drug targets. However, the dynamic nature of IDPs remains poorly understood …

The transcriptional coactivators CREB-binding protein (CBP) and p300 undergo a
particularly rich set of interactions with disordered and partly ordered partners, as a part of …

The protein folding problem was apparently solved recently by the advent of a deep learning
method for protein structure prediction called AlphaFold. However, this program is not able …

Many cellular proteins are intrinsically disordered and undergo folding, in whole or in part,
upon binding to their physiological targets. The past few years have seen an exponential …

The structure of a protein complex together with information about its affinity and other
thermodynamic characteristics provide a “frozen” view of the complex. This picture ignores …

Many eukaryotic proteins are disordered under physiological conditions, and fold into
ordered structures only on binding to their cellular targets. Such intrinsically disordered …

The mechanism of ligand binding coupled to conformational changes in macromolecules
has recently attracted considerable interest. The 2 limiting cases are the “induced fit” …