VASE

The "VASE" software tool is part of a broader initiative to enhance the resources available for biomedical research, particularly in protein structure bioinformatics. This initiative includes updates and expansions to a series of databases and tools that support the research on macromolecules. Notably, DSSP has been updated to analyze secondary structures of proteins, accommodating extremely large structures across multiple formats. The PDBREPORT database, known for listing anomalies in protein structures, has been overhauled to eliminate numerous minor issues, now offering reports in PDF format with computer-readable summaries.

VASE itself is introduced as a new addition, designed to analyze and visualize HSSP multiple sequence alignments for protein structures, thus providing a sophisticated tool for researchers in the field. Furthermore, the collection of databases known as "Lists" has been expanded, including a new database that assigns grades to protein structures based on their usefulness for bioinformatics projects.

Improvements have also been made to the PDB-REDO collection, which includes reanalyzed and re-refined protein structures solved by X-ray crystallography. These include enhancing the handling of sugar residues and hydrogen bonds and adding missing surface loops.