VCAb

This repository contains all the source code needed to generate the web interface and assembling the available experimental antibody structure space (Antibodies containing both V and C regions).

Access VCAb online

VCAb can be accessed online. For documentation on how to use the website, please go to the github wiki.

Generate local version of VCAb

VCAb shiny application

To generate the VCAb shiny app, go to shiny and run app.R.

Note

In order to run this code, BLAST must be installed in the command line. Please go to NCBI BLAST for more information.

VCAb antibody structural space

To collect the available experimental structural space of antibodies with both V and C regions, go to the vcab_db directory, run generate_db.py.

Note

1. generate_db.py should be run in python 3.
2. In order to run this code, BLAST must be installed in the command line. Please go to NCBI BLAST for more information.
3. generate_db.py would download PDB files and generate POPSComp results automatically by running bash scripts. Please make sure the pops.sh, deltaResidue.R (Modified from POPSR, please go to github for more information), pdb_download.sh (Modified from the script provided by RCSB pdb) are in the corresponding directories.
4. seq_db hold all the BLAST databases. Two files are under this directory: ref_db contains reference sequences for isotypes and light chain types collected from uniprot and won't be changed. vcab_db includes sequences in VCAb, which would be updated when generate_db.py is run.
5. anarci_vc is a package modified from anarci, used for antibody numbering for both V and C sequences. Please check github page for more information.

Packages required

file	Package	version
generate_db.py	pandas	1.2.1
generate_db.py	numpy	1.19.2
generate_db.py	Bio	1.79
generate_db.py	argparse	1.1
get_paired_seq.py	anarci_vc	modified from anarci, see github page
app.R	shiny	1.6.0
app.R	DT	0.17
app.R	rBLAST	0.99.2
app.R	taxonomizr	0.8.0
app.R	NGLVieweR	1.3.2
app.R	tibble	3.1.0
app.R	shinyhelper	0.3.2
app.R	ggplot2	3.3.3
app.R	dplyr	1.0.7