A new age in protein design empowered by deep learning
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Single-particle electron microscopy is a modern technique that biophysicists employ to learn the structure of proteins. It yields data that consist of noisy random projections of the protein structure in random directions, with the added complication that ...
The long term stability and the redox interaction between single walled carbon nanotubes (SWNTs) and photosynthetic reaction center proteins (RCs) purified from purple bacterium Rhodobacter sphaeroides R-26 in the SWNT/RC complex has been investigated. The ...
Two major milk whey proteins, β-lactoglobulin and α-lactalbumin, are among the main cowmilk allergens and can cause allergy even at a very low concentrations. Therefore, these proteins are interesting targets in food analysis, not only for food quality con ...
Modularity is at the core of bioinformatics. Here we focused on two different building blocks: protein domains and exons. While protein domains enable us to study the protein‚s functions, exons allow us to understand the evolution of the former. However, a ...
Pseudocontact shifts (PCSs) arise in para-magnetic systems in which the susceptibility tensor is anisotropic. PCSs depend upon the distance from the paramagnetic center and the position relative to the susceptibility tensor, and they can be used as structu ...
The HIV-1 Rev protein is responsible for shuttling partially spliced and unspliced viral mRNA out of the nucleus. This is a crucial step in the HIV-1 lifecycle, thus making Rev an attractive target for the design of anti-HIV drugs. Despite its importance, ...
We consider the interval constrained coloring problem, which appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy experiments is a method used to obtain information about pro ...
Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework ...
The economy of the production of lignocellulosic ethanol could be supported by the simultaneous use of different components of the biomass other than sugars. Among these, protein is present at high concentration in leaves and is a candidate for different p ...
In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...