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Found 13 papers, 4 papers with code
Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein-mimicking Nanoparticles
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and catalysis.
AI-predicted protein deformation encodes energy landscape
AI algorithms have proven to be excellent predictors of protein structure, but whether and how much these algorithms can capture the underlying physics remains an open question.
The Physical Logic of Protein Machines
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions.
AlphaFold2 can predict single-mutation effects
AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation effects?
General theory of specific binding: insights from a genetic-mechano-chemical protein model
Here, we present such a model that combines chemistry, mechanics and genetics, and explains how their interplay governs the evolution of specific protein-ligand interactions.
de novo gene birth as an inevitable consequence of adaptive evolution
Phylostratigraphy suggests that new genes are continually born de novo from non-genic sequences, and the genes that persist found new lineages, contributing to the adaptive evolution of organisms.
A topological look into the evolution of developmental programs
Here, we propose that these lineage maps can also reveal how developmental programs evolve: the modes of evolving new cell types in an organism should be visible in its developmental trajectories, and therefore in the geometry of its cell type lineage map.
Dimensional Reduction in Complex Living Systems: Where, Why, and How
The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems.
Walking droplets, swimming microbes: on memory in physics and life
Whirling and swerving, a bacterium is swimming in a test tube, foraging for food.
Structural asymmetry along protein sequences and co-translational folding
A phenomenological model predicts that CTF can be accelerated by asymmetry, up to double the rate, when folding time is commensurate with translation time; analysis of the PDB reveals that structural asymmetry is indeed maximal in this regime.
$αβ$ DCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone
Moreover, the interactions are strongly associated with the charge pattern: negatively charged regions in the destabilizing StpA N-terminal affect a few specific positions in the RNA, located in stems and in the pseudoknot.
Imperfect fifths pack into musical scales
Musical scales are used in cultures throughout the world, but the question as to how they evolved remains open.
Sound Audio and Speech Processing Neurons and Cognition
The self-referring DNA and protein: a remark on physical and geometrical aspects
All known life forms are based upon a hierarchy of interwoven feedback loops, operating over a cascade of space, time and energy scales.
