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Hyperspherical Prototypical Learning (HPL) is a supervised approach to representation learning that designs class prototypes on the unit hypersphere. The prototypes bias the representations to class separation in a scale invariant and known…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
In view of the important role helix-sheet transitions play in protein aggregation, we introduce a simple model to study secondary structural transitions of helix-coil-sheet systems using a Potts model starting with an effective Hamiltonian.…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
We consider a lattice model for amphiphiles in a solvent with molecules chemically similar to one part of the amphiphilic molecule. The dependence of the interaction potential on orientation of the amphiphilic molecules is taken into…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
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…
The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models.…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
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…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local…