Help/Glossary
- Reliable Fold Assignment
A reliable fold assignment is a fold assignment that corresponds to
a significant PSI-BLAST hit or to a reliable model. A PSI-BLAST hit
is significant when it is obtained in a filtered search and its E-value
is smaller than 0.0001. A reliable model is a model that is evaluated as good by a new
model evaluation procedure ( F. Melo, R. Sánchez, A. Sali. Statistical potentials for
fold assessment. Protein Science 11, 430-448, 2002. ). A model is predicted to be
good when the model score is higher than 0.7. A reliable model has a
probability of the correct fold that is larger than 95%. A fold is correct
when at least 30% of its C alpha atoms superpose within 3.5A
of their correct positions.
- Accurate Model
A model is predicted to be accurate when the sequence
identity between the target and the template is >= 30%.
- PSI-BLAST Fold Assignment
A PSI-BLAST fold assignment is a fold assignment that corresponds to
a significant PSI-BLAST hit. A PSI-BLAST hit is significant when it
is obtained in a filtered search and its E-value <= 0.0001 (green). An
E-value > 0.0001 (red) corresponds to insignificant PSI-BLAST hit. Thus,
a PSI-BLAST fold assignment can correspond to an unreliable model.
- Model Score
A new model score measure is currently being developed
(F. Melo, R. Sanchez, A. Sali, in preparation).
Model score is the probability that the model has
the correct fold and an approximately correct alignment. It ranges
from 0 to 1. Models with model score >= 0.7 (green) are considered
reliable; whereas those with model score < 0.7 (red) are considered
unreliable.
- Sequence Identity
Percentage of identical residues in the alignment between the target
and the template as reported during the template search. A model is
predicted to be good when the sequence identity between the target
and the template is >= 30% (green) and bad when it is < 30% (red).
This is NOT the sequence identity of the modeling alignment produced by
MODELLER.