Glasslike structure of globular proteins and the boson peak
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The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...
Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...
Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of glob ...
Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...
Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...
Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...
The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...
The opportunistic pathogen Pseudomonas aeruginosa adapts to solid surfaces to enhance virulence and infect its host. Type IV pili (T4P), long and thin filaments that power surface-specific twitching motility, allow single cells to sense surfaces and contro ...
Machine learning has provided a means to accelerate early-stage drug discovery by combining molecule generation and filtering steps in a single architecture that leverages the experience and design preferences of medicinal chemists. However, designing mach ...