Mapping antibody footprints using binding profiles

. 2023 Aug 22;3(8):100566. doi: 10.1016/j.crmeth.2023.100566

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

008-10 5G04	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
SFV019-2A02	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
045-09 2B05	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	PDB:7MEM
047-09 4G02	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	PDB:5W6G
SFV015-2F04	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
SFV009-3D04	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
029-09 4A01	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
030-09 2B03	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
045-09 2B06	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
047-09 4E01	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
051-09 4B02	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
051-09 5A02	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
CR-9114	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	PDB:5CJS
FI6	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	PDB:3ZTN
SC1000-3D04	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
SC1009-3B05	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
SC70-1F02	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
SC70-5B03	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
SFV005-2G02	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
030-09 1E05	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
047-09 1G05	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
051-09 4A03	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
051-09 5A01	contributed by Patrick Wilson and are described in many papers published elsewhere³⁶^,³⁷^,³⁸^,³⁹^,⁴⁰^,⁴¹^,⁴²^,⁴³^,⁴⁴^,⁴⁵^,⁴⁶^,⁴⁷^,⁴⁸^,⁴⁹	N/A
Alexa Fluor® 647 affinipure Donkey Anti-Human IgG (H + L)	Jackson ImmunoResearch	Cat#:709-605-149
Peroxidase-AffiniPure Goat Anti-Human IgG (H + L)	Jackson ImmunoResearch	Cat#:109–035-088

Chemicals, Peptides, and Recombinant Proteins

A/South Carolina/1/1918 H1N1 rHA	IRR	Cat#:FR-692; GenBank:AAD17229.1
A/WSN/1933 H1N1 rHA	Sino	Cat#:11692-V08H; GenBank:ACF54598.1
A/Puerto Rico/8/1934 H1N1 rHA	Sino	Cat#:11684-V08H; GenBank:ABD77675.1
A/Solomon Islands/3/2006 H1N1 rHA	Sino	Cat#:11708-V08H; GenBank:ABU99109.1
A/Brisbane/59/2007 H1N1 rHA	Sino	Cat#:11052-V08H; GenBank:ACA28844.1
A/California/07/2009 H1N1 rHA	Sino	Cat#:11085-V08H; GenBank:ACP41953.1
A/Michigan/45/2015 H1N1 rHA	Sino	Cat#:40567-V08H1; GenBank:APC60198.1
A/Brisbane/02/2018 H1N1 rHA	Native Antigens	Cat#:custom_EPI1440504; GISAID:EPI1440504
A/Aichi/2/1968 H3N2 rHA	Sino	Cat#:11707-V08H; GenBan::AAA43178.1
A/X-31/1968 H3N2 rHA	Sino	Cat#:40059-V08H; GenBank:P03438
A/Sydney/5/1997 H3N2 rHA	Sino	Cat#:40149-V08B; GenBank:ACO95259.1
A/Fujian/411/2002 H3N2 rHA	Sino	Cat#:40120-V08B; GenBank:AFG72823.1
A/California/7/2004 H3N2 rHA	Sino	Cat#:40118-V08B; GenBank:ABW80975.1
A/Wisconsin/67/2005 H3N2 rHA	Sino	Cat#:11972-V08H GenBank:ACF54576.1
A/Brisbane/10/2007 H3N2 rHA	Sino	Cat#:11056-V08H; GenBank:ABW23353.1
A/Hawaii/07/2009 H3N2 rHA	IRR	Cat#:FR-401; GenBank:ACT67781.1
A/Perth/16/2009 H3N2 rHA	Sino	Cat#:40043-V08H; GenBank:ACS71642.1
A/Victoria/210/2009 H3N2 rHA	Sino	Cat#:40058-V08B; GenBank:ADI52838.1
A/Switzerland/9715293/2013 H3N2 rHA	Sino	Cat#:40497-V08B; N/A
A/Maryland/26/2014 H3N2 rHA	N/A	N/A; N/A
A/Singapore/INFIMH-16-0019/2016 H3N2 rHA	Native Antigens	Cat#:custom_EPI1140322; GISAID::EPI1140322
A/Kansas/14/2017 H3N2 rHA	Native Antigens	Cat#:custom_AVG71503.1; GenBank:AVG71503.1
B/Malaysia/2506/2004 B rHA	Sino	Cat#:11716-V08H; GenBank:ACO05957.1
B/Florida/4/2006 B rHA	Sino	Cat#:11053-V08H; GenBank:ACA33493.1
B/Brisbane/60/2008 B rHA	Sino	Cat#:40016-V08H; GenBank:ACN29380.1
B/Phuket/3073/2013 B rHA	Sino	Cat#:40498-V08B; GenBank:ANK57684.1
B/Colorado/06/2017 B rHA	Native Antigens	Cat#:custom_ARQ85589; GenBank:ARQ85589
A/Hong Kong/483/1997 H5N1 rHA	Sino	Cat#:11689-V08H; GenBank:AAC32099.1
A/Anhui/1/2005 H5N1 rHA	Sino	Cat#:11048-V08H1; GenBank:ABD28180.1
A/Indonesia/5/2005 H5N1 rHA	Sino	Cat#:11060-V08B; GenBank:ABW06108.1
A/Bar-headed goose/Qingi/14/2008 H5N1 rHA	Sino	Cat#:11059-V08B1; GenBank:ACL28277.1
A/Guineafowl/Hong Kong/WF10/1999 H9N2 rHA	Native Antigens	Cat#:FLU-H9N2-HA-100; GenBank:AOT22363.1
A/Hong Kong/1073/1999 H9N2 rHA	Sino	Cat#:11229-V08H; GenBank:NP_859037.1
A/Anhui/1/2013 H7N9 rHA	Sino	Cat#:40103-V08H; N/A
A/Shanghai/1/2013 H7N9 rHA	Sino	Cat#:40104-V08H; GenBank:YP_009118475
A/Japan/305/1957 H2N2 rHA	Sino	Cat#:11088-V08H; GenBank:AAA43185.1
A/mallard/Ohio/657/2002 H4N6 rHA	Sino	Cat#:11714-V08H; GenBank:ABI47995.1
A/chicken/Hong Kong/17/1977 H6N4 rHA	Sino	Cat#:40027-V08H; GenBank:CAC84244.1
A/New York/107/2003 H7N2 rHA	IRR	Cat#:FR-69; N\A
A/Netherlands/219/2003 H7N7 rHA	Sino	Cat#:11082-V08B; GenBank:AAR02640.1
A/pintail duck/Alberta/114/1979 H8N4 rHA	Sino	Cat#:11722-V08H; GenBank:ABB87729.1
A/mallard/Minnesota/Sg-00194/2007 H10N3 rHA	Sino	Cat#:40184-V08B; GenBank:ACT84107.1
A/mallard/Alberta/294/1977 H11N9 rHA	Sino	Cat#:11704-V08H; GenBank:ABB87228.1

Software and Algorithms

MUSCLE	EML-EBI	https://doi.org/10.1093/nar/gkh340
In-house python script ncluding mAb-Patch	This paper	http://doi.org/10.5281/zenodo.7947980
PyMOL2	The PyMOL Molecular Graphics System, Version 2 Schrödinger, LLC	https://pymol.org/2
ZDock Server	Pierce et al.⁵⁷	https://doi.org/10.1093/bioinformatics/btu097