Related papers: Designability and Thermal Stability of Protein Str…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…
Why are materials with specific characteristics more abundant than others? This is a fundamental question in materials science and one that is traditionally difficult to tackle, given the vastness of compositional and configurational space.…
The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
Uncovering the formation process that reproduces the distinct properties of compact super-Earth exoplanet systems is a major goal of planet formation theory. The most successful model argues that non-resonant systems begin as resonant…
Many cellular patterns exhibit a reaction-diffusion component, suggesting that Turing instability may contribute to pattern formation. However, biological gene-regulatory pathways are more complex than simple Turing activator-inhibitor…
Standard optimality criteria (e.g. A-, D-optimality criterion, etc.) have been commonly used for obtaining optimal designs. For a given statistical model, standard criteria assume the error variance is known at the design stage. However, in…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…