HIV-1 Broadly neutralising antibodies (bnAbs) reactive epitopes viewer

This app prototype for displaying bNABs epitope data by participant

The following layout was used as a template for displaying data.

Reference: Bhavna Hora, et al. Neonatal SHIV infection in rhesus macaques elicited heterologous HIV-1-neutralizing antibodies. Cell Reports. 2021.

Data follows the structure below:

HIV-1 envelope-reactive broadly neutralizing antibody (bnAb) epitopes

Epitope	Env location	Residues (amino acids/ regions)	References	epitopeID
CD4-binding site	276-282	Loop D; key contacts - PNGS (N*S/T) N279-280	West et al, PNAS, 2012	Loop D
CD4-binding site	365-371	CD4-binding site (bs) loop; key contact - D368	West et al, PNAS, 2012	bs loop
CD4-binding site	456-469	V5 loop; key contact – R456	West et al, PNAS, 2012	V5 loop
V2-apex	166	Arginine (R)	Andrabi et al., Immunity, 2015	V2-apex
V2-apex	168-171	Lysine (K)-rich	Haynes et al., Nat Immunol Rev., 2022	V2-apex
V2-apex	156, 160	PNGS (N*S/T)	Haynes et al., Nat Immunol Rev., 2022	V2-apex
V3-glycan	301, 332	PNGS (N*S/T)	Haynes et al., Nat Immunol Rev., 2022	V3-glycan
V3-glycan	324-327	GDIR	Haynes et al., Nat Immunol Rev., 2022	V3-glycan
Gp41 MPER	662-667	ELDKWA	Munir, Haynes, et al. (Duke)	Gp41-1
Gp41 MPER	671-676	NWFNIT	Munir, Haynes, et al. (Duke)	Gp41-1
Gp41 fusion peptide	512-527	AVGIGAVFLGFLGAAG	Kong et al., Science, 2016	Gp41-2
Gp120-gp41 interface	611 (gp41)	PNGS (N*S/T)	Falskowka et al., Immunity, 2014	Interface-1
Gp120-gp41 interface	637 (gp41)	PNGS (N*S/T)	Falskowka et al., Immunity, 2014	Interface-2
Gp120-gp41 interface	276 (gp120)	PNGS (N*S/T)	Falskowka et al., Immunity, 2014	Loop D
Gp120-gp41 interface	448 (gp120)	PNGS (N*S/T)	Falskowka et al., Immunity, 2014	Interface-3

NB: (1) PNGS – potential N-linked glycosylation site; (2) residues are listed as amino acids

Installation and running:

1. Ensure your Docker client is running

2. Run the following commands in this directory:

   docker-compose v.1.xx

   docker-compose build

   docker-compose up

   docker-compose v.2.xx

   docker compose build

   docker compose up

Note: This does not show changes made to the code without a rebuild.

3. Open a webpage at localhost:3000

Uninstall

Run the following command in this directory:

docker-compose v.1.xx

docker-compose down

docker-compose v.2.xx

docker compose down