Despite advances in machine learning-based protein structure prediction, we are still far
from fully understanding how proteins fold into their native conformation. The conventional …

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 …

All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Biomolecules are the prime information processing elements of living matter. Most of these
inanimate systems are polymers that compute their own structures and dynamics using as …

A predictive coarse-grained protein force field [associative memory, water-mediated,
structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the …

Neighbouring domains of multidomain proteins with homologous tandem repeats have
divergent sequences, probably as a result of evolutionary pressure to avoid misfolding and …

Proteins that fold cotranslationally may do so in a restricted configurational space, due to the
volume occupied by the ribosome. How does this environment, coupled with the close …

Natural protein molecules are exceptional polymers. Encoded in apparently random strings
of amino-acids, these objects perform clear physical tasks that are rare to find by simple …

Molecular evolution has focused on the divergence of molecular functions, yet we know little
about how structurally distinct protein folds emerge de novo. We characterized the …

Computational simulations of protein folding can be used to interpret experimental folding
results, to design new folding experiments, and to test the effects of mutations and small …