SAbPred: SCALOP

Sequence-based antibody CAnonical LOoP structure annotation.

SCALOP is a sequence-based canonical form predictor for five of the six complementarity-determining regions (H1, H2, L1, L2 and L3) on an antibody.
Submit a single or multiple sequence(s) through the form below.
The sequences will be numbered by ANARCI and assigned to canonical forms by SCALOP.
Results are displayed by the name of the assigned clusters and the PDB-chain identifier from which the median structure of the assigned cluster is extracted. (Load an example result)
Where no result is shown for a given sequence, it is not considered an antibody by ANARCI, thus no assignment is made.
If the user supplies a framework structure (in the same numbering scheme), CDR loop structures are selected from the members of the assigned cluster and grafted onto the supplied framework.
SCALOP does not detect clashes nor predict side chain conformations in the grafted loops. Please use ABodyBuilder to generate a complete model.

SCALOP is freely available to download for all users.

Submit a single antibody chain sequence (or two chains separated by / ):

or upload multiple sequences as a fasta file:

Choose a numbering scheme:

IMGT Chothia

Choose a CDR definition:

North IMGT Chothia

Upload a framework structure (optional):

download example

Heavy chain ID:
Light chain ID:

SCALOP is freely available for all users.
Upon download, all previous databases will be included.
It runs on Linux and OSX.
If you would like to be kept informed about new releases of the software, please fill out the form below.

﹡Email address:

﹡Institution:

Dependencies

Installation

tar -zxvf scalop-1.0.tar.gz

cd scalop-1.0

python setup.py install

Users without root permissions can use either of the following commands instead:

python setup.py install --user

python setup.py install --home="~"

Usage

SCALOP -i EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSS...

...LTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSA

Yearly updates are available for previous years; monthly updates up to the previous month are available for the current year only.
Databases should be saved in the 'database' directory in the module path of SCALOP (e.g. /lib/python2.7/site-packages/scalop/database).

Year:
Month:

Choose a numbering scheme:

IMGT Chothia

Choose a CDR definition:

North IMGT Chothia