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 (multiple sequences upload has priority).
  • 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 generate a complete model.



SCALOP is freely available for all users.
Software Download

Copy and paste a single sequence [Help]

or






Options

Choose numbering scheme:


Choose CDR definition:



Downloads

Source code

  • SCALOP and ANARCI are 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 (?)






Dependencies

Install

  • Unpack:
    tar -zxvf scalop-1.X.tar.gz

  • Run:
    cd scalop-1.X
    python setup.py install

  • Users without root permissions can refer to this page.

Usage

  • For details of how to use the software see the README file
  • Example: SCALOP -i EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSA


Database

  • 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 (YYYY):
Month (MM):
Choose numbering scheme:

Choose CDR definition: