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From CAGT

Documentation for Consensus

Consensus Documentation


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.

 

Strength

Explanation

9-7

These regions are the most reliable according to the alignment. Regions with a score of 9 are more reliable than those of 7. They correspond to an agreement between at least the top three of the five component methods used, while the latter correspond to an agreement between any three of the five methods (excluding pairs of consensus 9). These regions are typically safe to copy from the template.

6-5

Only two of the five methods agree (excluding pairs of higher consensus strengths). These regions are not extremely robust alignment regions but may be selected for modeling subject to certain structural criteria.

4-0

There is no agreement between the five component alignments for these regions. They are unreliable for modeling by default unless selected based on neighboring selections and structural criteria.

-5

No alignment method has aligned this pair. Just arbitrarily paired up to get as complete an alignment as possible. They are not at all reliable for modeling.

*** 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

Target

Template

 

Target

Template

1aerA

1ddt

 

1c3oA

1g8mA

1lckA

2shpA

 

1zymA

1dik

1qoxN

1qvbA

 

1cjcA

1qjdA

1hfc

1sat

 

2cuaA

1qniA

1cz4A

1e32A

 

1tf4A

1nbcA

1e5gA

1qubA

 

1a9nA

1dceA

1b91A

1eqfA

 

1bvyF

1amoA

8fabA

1cd8

 

1hxn

1qhuA

1pii

1nsj

 

1mml

1rthA

8fabA

1iakA

 

1it2A

1abwA

1iknD

1ycsB

 

1a0p

1aihA

1hcl

1fmk

 

1cyx

2occB

8fabA

1hxmA

 

1dleA

1ucyH

1lckA

1a81A

 

1gdoA

1ecfB

8fabA

1igtB

 

1i6wA

1cvl

1qoxN

1e70M

 

1fit

1emsA

1dk5A

1avc

 

1uok

1bvzA

1g24A

1qs1A

 

1fchA

1hxiA

1larA

2shpA

 

1im5A

1yacA

1iknD

2myo

 

2vhbA

1cqxA

8fabA

1tvdA

 

1dgsA

1b04A

1c0aA

1lylA

 

1h9jA

1b9mA

2prd

1wgjA

 

1cxqA

1b9dA

1f16A

1maz

 

1d4vA

1extA

1rtm1

1esl

 

1tml

1bvwA

1pii

1a53

 

1fgkA

1b6cB

1tfe

1efuB

 

1hdhA

1auk

1pcl

1qcxA

 

1qlaA

1chuA

1hcl

1cdkA

 

1g2qA

1qb7A

1larA

1pty

 

1hqoA

1e6bA

2er7E

1fknA

 

1hd8A

1skf

1theB

1cs8A

 

1ivyA

1ac5

8fabA

1tcrA

 

1qagA

1bkrA

1e6wA

1b16A

 

1b5l

1ifa

8fabA

1mfa

 

1cr5A

1qcsA

1gaxA

1ile

 

1eggA

1ixxB

1c0aA

1b8aA

 

2tnfA

1aly

3pchA

3pchM

 

1etpA

1fcdC

1bj7

1obpA

 

1hp0A

2masA

1pcl

1air

 

1ft1B

1dceB

1cfe

1qnxA

 

1qouA

1a44

1rtm1

1htn

 

1hr6A

1be3A

1iq4A

1ffkD

 

5tmpA

3tmkA

1nox

1bkjA

 

1hcuA

1dl2A

2er7E

1eagA

 

1cpq

1bbhA

3prn

2por

 

1ksiB

1a2vA

1fiqC

1alo

 

1k3fA

1ecpA

1bolA

1bk7A

 

1iakB

1hdmB

1csh

1aj8A

 

1euhA

1bpwA

2lbd

2prgA

 

1pov1

1aym1

3dfr

1aoeA

 

 

 

1nf1A

1wer

 

 

 

1ithA

2hbg

 

 

 

1ew4A

1dlxA

 

 

 

1sek

1c8oA

 

 

 

1pmaP

1pmaA

 

 

 

2er7E

2rmpA

 

 

 

1at3A

1lay

 

 

 

1sfe

1mgtA

 

 

 

1bylA

1ecsA

 

 

 

8fabA

1bec

 

 

 

1hcl

1ia8A

 

 

 

1e6wA

1ybvA

 

 

 

1ig3A

1ig0A

 

 

 

1e6wA

1cydA

 

 

 

1bw0A

1bjwA

 

 

 

2lbd

1lbd

 

 

 

2lbd

1db1A

 

 

 

8fabA

32c2A

 

 

 

1bj7

1mup

 

 

 

1hcl

1a6o

 

 

 

1e6wA

1bdb

 

 

 

3dfr

1d1gA

 

 

 

8fabA

1gc1H

 

 

 

1cpt

1rom

 

 

 

3dfr

1vdrA

 

 

 

5ptp

1a7s

 

 

 

1qi7A

1d6aB

 

 

 

5ptp

8kme2

 

 

 

 

Protein Engineering