SCALOP (Python 3) Sequence-based antibody Canonical LOoP structure annotation
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 northExample 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
2018 Wing Ki Wong Dr Jinwoo Leem Prof Charlotte M. Deane - Oxford Protein Informatics group.
Contact [email protected]