Protein folding has been viewed as a difficult problem of molecular self-organization. The
search problem involved in folding however has been simplified through the evolution of …

Proteins are increasingly used in basic and applied biomedical research. Many proteins,
however, are only marginally stable and can be expressed in limited amounts, thus …

We apply unsupervised machine learning techniques, mainly principal component analysis
(PCA), to compare and contrast the phase behavior and phase transitions in several …

The protein frustratometer is an energy landscape theory-inspired algorithm that aims at
localizing and quantifying the energetic frustration present in protein molecules. Frustration …

The associative memory, water-mediated, structure and energy model (AWSEM) has been
successfully used to study protein folding, binding, and aggregation problems. In this work …

Intrinsically disordered proteins (IDPs) constitute a significant fraction of eukaryotic
proteomes. High-resolution characterization of IDP conformational ensembles can help …

To function, biomolecules require sufficient specificity of interaction as well as stability to live
in the cell while still being able to move. Thermodynamic stability of only a limited number of …

The nucleosome is the fundamental unit for packaging the genome. A detailed molecular
picture for its conformational dynamics is crucial for understanding transcription and gene …

Using a predictive coarse-grained protein force field, we compute and compare the free
energy landscapes and relative stabilities of amyloid-β protein (1–42) and amyloid-β protein …

The prevailing current view of protein folding is the thermodynamic hypothesis, under which
the native folded conformation of a protein corresponds to the global minimum of Gibbs free …