SCALOP

Description

SCALOP (Python 3) Sequence-based antibody Canonical LOoP structure annotation

Installation

The easiest way to install SCALOP dependencies is using conda:

git clone https://github.com/oxpig/SCALOP.git
conda create -n scalop-env python=3.8 -y
conda activate scalop-env
conda install -c bioconda numpy pandas hmmer biopython -y
pip install SCALOP/

Input format

• Single complete antibody sequence
• Complete heavy and light chain sequences separated by ‘/‘
• Fasta file

Example Command line tool

SCALOP -i VKLLEQSGAEVKKPGASVKVSCKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKYSQKFRGRVTFTRDTSATTAYMGLSSLRPEDTAVYYCARDPYGGGKSEFDYWGQGTLVTVSS/ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV --scheme imgt --definition north

Example Python module

from scalop.predict import assign
input='VKLLEQSGAEVKKPGASVKVSCKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKYSQKFRGRVTFTRDTSATTAYMGLSSLRPEDTAVYYCARDPYGGGKSEFDYWGQGTLVTVSS/ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIKRTV'
assign(input)

Dependencies

• HMMER 3.1b2 (February 2015); http://hmmer.org/
• numpy v. 1.10+
• pandas

Authors

2018 Wing Ki Wong Dr Jinwoo Leem Prof Charlotte M. Deane - Oxford Protein Informatics group.

Contact opig@stats.ox.ac.uk