While working with the service, one should keep in mind that:
- PISA is not a curated source of data, but rather presents
results calculated by certain physico-chemical models
for PDB and/or uploaded macromolecular structures.
- Estimates for macromolecular-ligand interactions in PISA are
less precise than those for macromolecular-macromolecular
interactions. Ligands in PISA are effectively considered as surface
modifiers (fixed to the macromolecular surface), unless that is
not possible due to symmetry of interactions. Fixed ligands
are not included into the dissociation pattern.
- PISA relies on the correctness of coordinate files submitted.
"Correctness" implies not only a formal compliance with
the file format, but also using standard names for atoms and
residues. Using trivial names prevents PISA of getting data
from the database, which will result in ignoring these
- Incomplete coordinate files (such as backbone-only) are not
suitable for PISA unless only a few residues from many are affected.
- PISA uses identical computational procedures for PDB
entries and user uploads.
- The physical-chemical models, used in PISA, are implemented
with a finite precision in the mathematical sense. As a result,
some figures may not add up precisely. For example, the calculation
of surface area produces slightly different results at different
orientations of the molecule.
- It is stated, however, that to the best knowledge and belief
of the authors, the finite precision of implementation does
not result in artifacts beyond those inherent in the used models.
- The models, used in PISA, have their validity limits. Therefore
the results, such as macromolecular oligomeric states, should be
rated as probable. It is estimated that oligomeric states are
correct in 85-90% of instances, however, there is no hard evidence
to prove or disprove this figure.
- PISA models include calibration parameters that are tuned
in order to achieve a higher probability of correct answers.
From time to time these parameters may change, which will cause
a change in the resulting figures. It is expected, however, that
this change will not be significant in most instances.
- Interface structural searches are based on
technology, which employs certain similarity thresholds. It is
therefore possible that some lower-similarity matches, which
may still be of interest, are missed by the service.