Related papers: On correlation between protein secondary structure…

What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…

By folding into particular 3D structures, proteins play a key role in living beings. To learn meaningful representation from a protein structure for downstream tasks, not only the global backbone topology but the local fine-grained…

This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…

Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

We introduce a model of proteins in which all of the key atoms in the protein backbone are accounted for, thus extending the Freely Rotating Chain model. We use average bond lengths and average angles from the Protein Databank as input…

Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in…

Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…

In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…

Determining the three-dimensional structure of a protein from its amino-acid sequence remains a fundamental problem in biophysics. The discrete Frenet geometry of the C$_\alpha$ backbone can be mapped, via a Hasimoto-type transform, onto a…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…

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…

Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…

We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is…

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 the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year…

The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent…

The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…