INPUT

The input_files directory contains the input files used by the server
in the correct format.

OUTPUT

The contacts file provides the contact probabilities for all the
protons pairs in the protein (excluding contacts between protons from
the same residue). Two contact probabilities are provided, a direct
and an implied probability. The direct probability comes from the
interpretation of spectral crosspeaks that directly arise, or could
arise from the proton contact. In other words, given a starting prior
probability for the contact, the direct contact probability is the
resulting posterior probability after the Bayesian interpretation of
the spectra. Since contact probabilities between protons for any given
pair of residues are correlated, one can also calculate the
probability of a pair of protons being in contact (<5 A) from the
contact probabilities of the other related protons. This is the
implied probability. The direct probabilities are more accurate, but
the implied probabilities provide both a consistency check and allow
inferences to be made indirectly in cases where the spectra provide
little direct information due to chemical shift degeneracy for
example. Only contacts with probabilities >0.001 are displayed.

The peaks file provides similar information as the contacts files but
organised by the crosspeaks. The Bayesian method does not assign
crosspeaks in the traditional sense but derives contact probabilities
from the crosspeaks. Again, both the direct and implied probabilities
are given and only those contacts with probabilites > 0.001 are shown.

The ss file gives the predicted secondary structure of the protein as
derived from PsiCSI. PsiCSI not only provides a prediction but also
estimated probabilities for each of the three secondary structure
states which are used to calculate the initial proton contact
probabilities.

We also provide a directory (cyana_files) with a cyana constraints
file derived from the contact probabilities and a simple cyana script
and the support files needed to generate an ensemble of structures
using cyana (version 2-1).
