Secondary Structure Elements - Annotations and Schematic 2D Visualizations Stable for Individual Protein Families

APPENDIX 2: Schematic Diagrams of Secondary and Tertiary Structure Elements

Importance of Secondary Structure Elements for Prediction of Go Annotations

Predicted or actual protein secondary structure, in addition to amino acid sequence, is often used for fold recognition and function prediction. Different kinds of secondary structure elements could be predicted with different accuracy by different prediction methods and this could affect the fold or function prediction performance. In this study, contribution of amino acid sequence residues be...

Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature

Protein structure visualization tools render images that allow the user to explore structural features of a protein. Context specific information relating to a particular protein or protein family is not easily integrated and must be uploaded from databases or provided through manual curation of input files. We describe a mixed natural language processing and sequence analysis based approach fo...

Automatic Protein Structure Clustering Using Secondary Structure Elements

Positive Selection Differs between Protein Secondary Structure Elements in Drosophila

Different protein secondary structure elements have different physicochemical properties and roles in the protein, which may determine their evolutionary flexibility. However, it is not clear to what extent protein structure affects the way Darwinian selection acts at the amino acid level. Using phylogeny-based likelihood tests for positive selection, we have examined the relationship between p...