Key trends

Is quality of biomacromolecules on the rise?

On the basis of relationships between the year of release and various quality factors of biomacromolecular structures, we can see that quality of biomacromolecular structures is improving in time. An example of such trend is depicted in the plot below, where relationship of the clashscore structure quality factor and the year of release factor is visualized. The lower is the value of clashscore, the higher is the quality of a structure.

Does size of a biomacromolecule influence its quality?

In ValTrendsDB, size of a biomacromolecule can be represented using several size factors (e.g., molecular weight, number of atoms, and number of residues). Most relationships between biomacromolecule size and quality factors show prevalent trend that quality decreases with increasing size (of course, there are exceptions to this trend). This trend is shown in the plot below, where relationship of the sidechain outliers structure quality factor and the structure atom count (without ligand atoms) factor is visualized. The lower is the percentage of sidechain outliers in a structure, the higher is the quality of such structure.

Does resolution of a biomacromolecule influence its quality?

An interesting question is what influence resolution has on quality of models of biomacromolecular structures that have been obtained using X-ray crystallography. Relationships of biomacromolecule structure quality factors mostly show a significant trend (with a few exceptions such as this one): The lower the resolution is, the lower the quality is. This trend is shown in the plot below, where relationship of the clashscore structure quality factor and the structure resolution factor is visualized. The lower is the value of clashscore, the higher is the quality of a structure.

Is quality of ligands on the rise?

The situation regarding quality improvement is more complicated when dealing with ligands instead of biomacromolecules. Some relationships show increase of quality in time, while other relationships even show decline of quality of ligands in time. Most relationships, however, point to the trend that quality of ligand structures is stagnating. This trend is shown in the plot below, where relationship of the average ligand RSCC ligand quality factor and the year of release is visualized. The higher is the value of RSCC, the higher is the quality of a ligand. Please note that the RSCC quality metric is only relevant to structures of biomacromolecular complexes that were obtained using X-ray crystallography.

Does size of ligands influence their quality?

For ligands, the trend that their quality decreases with increasing size and complexity is similar to the one that biomacromolecules have. This trend is shown in the plot below, where relationship of the quality factor average RSR of ligands in structure and the size factor average ligand size in structure factor is visualized. The lower is the value of RSR, the higher is the quality of a ligand model.

However, it is not as straightforward, as is regularly the case with ligands and their trends. A decent amount of ligand quality factors show weak or nonexistent relationships with ligand size and complexity factors. Most of these ligand quality factors are sourced from data of the ValidatorDB database (example relationship is here).

Does resolution of a ligand influence its quality?

Similar trend to the one biomacromolecules have exists for ligands as well. Relationships of ligand structure quality factors, sourced from wwPDB Validation Reports, show a significant trend: The lower the resolution is, the lower the quality is. This trend is shown in the plot below, where relationship of the average RSR of ligands in structure ligand quality factor and the structure resolution factor is visualized. The lower is the value of RSR, the higher is the quality of a ligand model.

On the other hand, ligand structure quality factors, sourced from the ValidatorDB database, have only moderate relationships with structure resolution at best (as can be seen in this plot).