Amino Acids in Nine Ligand-Prefer Ramachandran Regions

Amino Acids in Nine Ligand-Prefer Ramachandran Regions

Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analy...

Minimal Immunogenic Epitopes Have Nine Amino Acids

Background

Highly expressed proteins prefer less informative amino acids

The transcriptional and translational systems are essentially information processing systems. However, how to quantify the amount of information decoded during expression remains a mystery. Here, we have proposed a simple method to evaluate the amount of information transcribed and translated during gene expression. We found that although proteins with a high copy number have more information t...

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

Distributions of the backbone dihedral angles of proteins have been studied for over 40 years. While many statistical analyses have been presented, only a handful of probability densities are publicly available for use in structure validation and structure prediction methods. The available distributions differ in a number of important ways, which determine their usefulness for various purposes....

Amino Acids Specifying MHC Class Preference in TCR Va2 Regions