Related papers: On correlation between protein secondary structure…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
An electronic orbital of a dihedral angle of a molecular chain is introduced. A tight-binding Hamiltonian on the basis of the dihedral orbitals is defined. This yields the Green's function between two dihedral angles of the chain. It is…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
Despite recent advancements in deep learning methods for protein structure prediction and representation, little focus has been directed at the simultaneous inclusion and prediction of protein backbone and sidechain structure information.…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Protein secondary structure prediction is an important problem in bioinformatics. Inspired by the recent successes of deep neural networks, in this paper, we propose an end-to-end deep network that predicts protein secondary structures from…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the left-handed helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Complex supermanifold structures being deformations of the exterior algebra of a holomorphic vector bundle, have been parametrized by orbits of a group on non-abelian cohomology by P. Green. For the case of odd dimension $4$ and $5$ an…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Apart from the knots formed by the main-chain, the proteins can form numerous topological structures, when included the covalent and ion-mediated interactions. In this work, we define the protein non-trivial $\theta$-curves and identify 7…