Related papers: Topological features of proteins from amino acid r…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
The distribution of human linguistic groups presents a number of interesting and non-trivial patterns. The distributions of the number of speakers per language and the area each group covers follow log-normal distributions, while population…
We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Hierarchical materials in the natural world are often made through the self-assembly of amphiphilic molecules. Achieving similar structural complexity in synthetic materials requires understanding how various molecular parameters affect…
Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affect hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size…
Protein-protein interaction networks associated with diseases have gained prominence as an area of research. We investigate algebraic and topological indices for protein-protein interaction networks of 11 human cancers derived from the…
Thresholding--the pruning of nodes or edges based on their properties or weights--is an essential preprocessing tool for extracting interpretable structure from complex network data, yet existing methods face several key limitations.…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
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…
The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Aggregation of amphiphiles through the action of hydrophobic interactions is a common feature in soft condensed matter systems and is of particular importance in the context of biophysics as it underlies both the generation of functional…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…