Documentation for Consensus

Usage

Note: - If no template is specified, the server picks a template by using a method similar to PDB-BLAST.

We would like to note however, that template identification is not a strength of the server. Therefore, it is best if the template is supplied.

Explanation for the columns in the consensus output

Columns 1-2 correspond to the target.
Columns 3-4 correspond to the template.
Column 5 is the consensus strength (0-9) for that pair of aligned residues according to sequence alignments
Column 6 is the selection status. An� 'S'� indicates that the corresponding pair of residues has been confidently aligned and may be used in comparative

modeling. A� '.'� indicates otherwise.
Please disregard column 7. This is only for diagnostic purposes and will soon be removed.

Meaning of the consensus strength

The reliability of each position in the alignment is assigned a score from 0-9. Higher score indicates a greater reliability of the alignment at that position.

However, even a score of 9 does not necessarily mean that it is safe to model that region from the template. The score, along with other structural factors

are used to select the regions reliable for modeling, indicated with an “S” in the output. The term “reliable” in this context implies that the model generated

for only the reliable regions will most likely have less than 3 � rms distance from the native structure of the target.

The consensus strength is assigned based on the agreement between the component alignment methods for that position.

If you are interested in greater detail, then here is the explanation.

*** All pairs of lower consensus strengths are ensured to be sequentially compatible with pairs of higher consensus strength.

Bugs

There may be bugs, although we have ironed out all those we detected so far. If you believe that some part of the output is very obviously erroneous,

or there is no output at all, please let us know. We know that there are some limitations. If you have any suggestions or wish-list regarding the format of

the output or the capabilities of the server, we will appreciate if you email us.

If your job is the first request in the queue, the webpage may deceptively seem as if it is still loading the results, but they will be sent via email.

Please Cite

Consensus alignment for reliable framework prediction in homology modeling.
J.C. Prasad, S. R. Comeau, S. Vajda, and C.J. Camacho.   Bioinformatics 2003 19: 1682-1691. Click here to download.

Our server's performance at CAFASP3 according to Contact Prediction Evaluation

Protein pairs used for method development

�� Training set������������������� Validation set