QUANTA - Protein Design and Protein Health
Protein Design
Protein Design is a versatile application for modeling and analyzing protein structures. There are two major palettes associated with this application— Protein Design and Protein Utilities.
The Protein Design palette contains 18 options that can be classified into three types of utilities:
- Modeling utilities: allow users to align and superpose sequences and structures, create homology models, edit the protein, model backbone and sidechains, predict secondary structure and superpose folding motifs
- Analysis utilities: provide tools for analyzing domain and secondary structure, calculating accessibility, displaying contact maps and performing a profile analysis (which allows the user to determine invalid and misfolded structure regions)
- Databases utilities: includes searching motifs, sequence databases, and structure databases
The Protein Utilities palette, which contains visual tools and structure checks, is a means for accessing the Protein Health utility that is described below.
Protein Design can be purchased as part of the QUANTA Protein Modeling package, which also contains the Protein Health utility described below.
Protein Health
The Protein Health utility helps to identify features in a protein structure that are uncommon or incorrect and therefore warrant closer examination, such as the wrong chirality of Ca atoms, main chain conformations that fall outside accepted regions on the Ramachandran map, or side chain conformations that do not correspond to regularly observed rotamers. This application aids in model building and can provide criteria for judging the quality of imported data, such as PDB files. Other functionality includes calculating automatically buried polar atoms and hydrophilic regions, exposed hydrophobic regions, close contact, and holes within the protein.
Protein Health can be purchased along with Protein Design as part of the QUANTA Protein Modeling package, or it ca be purchased on its own.
