Related papers: Structure calculation strategies for helical membr…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
We propose an improved prediction method of the tertiary structures of $\alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because…
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the transmembrane helix regions are obtained from one of existing…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with 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…
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer…
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…
For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as…
An effective model for protein structures is important for the study of protein geometry, which, to a large extent, determine the functions of proteins. There are a number of approaches for modelling; one might focus on the conformation of…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Protein structure prediction remains a challenge in the field of computational biology. Traditional protein structure prediction approaches include template-based modelling (say, homology modelling, and threading), and ab initio. A…