Related papers: A geometrical framework for thinking about protein…

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…

A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…

In many networks, including networks of protein-protein interactions, interdisciplinary collaboration networks, and semantic networks, connections are established between nodes with complementary rather than similar properties. While…

Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions using the edge simplices from alpha shape of…

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.…

The evolutionary fitness landscape of biological molecules is extremely sparse and heterogeneous, with functional sequences forming isolated dense ``islands'' within a vast combinatorial space of largely non-functional variants. Protein…

Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…

Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…

A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…

We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…

We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to…

Many types of peripheral and transmembrane proteins can sense and generate membrane curvature. Laterally isotropic proteins and crescent proteins with twofold rotational symmetry, such as Bin/Amphiphysin/Rvs superfamily proteins, have been…

A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…

The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…

Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…

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…

The surrounding world surprises us by the beauty and variety of complex shapes that emerge from nanometric to macroscopic scales. Natural or manufactured materials (sandstones, sedimentary rocks and cement), colloidal solutions (proteins…

Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…