Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools

Dewaker, Varun; Morya, Vivek Kumar; Kim, Yoo Hee; Park, Sung Taek; Kim, Hyeong Su; Koh, Young Ho

doi:10.1186/s40364-025-00764-4

Biomarker Research

Table 2 Developed Tools and their Applications

From: Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools

S. No	Tools/Model	Year	Function/Role	GitHub link	Reference
Structural Prediction of CDRs
1	AbFlex	2024	CDR design method with a given antibody-antigen complex	https://github.com/wsjeon92/AbFlex	[289]
2	AbDiffuser	2023	Generation of antibody 3D structures and sequences	Not Mentioned	[290]
3	ImmuneBuilder/ ABodyBuilder2/ NanoBodyBuilder2 TCRBuilder2	2023	Fv modelling, antibody structure modeling, TCR structure modelling, nanobody structure modelling	https://github.com/oxpig/ImmuneBuilder https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred	[291]
4	IgFold	2022	Fast, accurate antibody structure prediction	https://github.com/Graylab/IgFold	[24]
5	ABLooper	2022	Antibody CDR loop structure prediction	https://github.com/oxpig/ABlooper	[147]
6	DeepSCAb	2022	Prediction of antibody backbone and side-chain conformations	https://github.com/Graylab/DeepSCAb	[292]
7	DeepAb	2022	Antibody structure prediction	https://github.com/RosettaCommons/DeepAb	[88]
8	SMCDiff	2022	Protein backbones and motif-scaffolding	https://github.com/blt2114/ProtDiff_SMCDiff	[293]
9	DeepH3	2020	Prediction of CDR H3 loop	https://github.com/Graylab/deepH3-distances-orientations	[148]
10	RosettaAntibody	2018	Antibody modelling	https://www.rosettacommons.org/ https://github.com/RosettaCommons/rosetta	[82]
11	AlphaFold		Structure prediction and modelling	https://github.com/google-deepmind/alphafold	[28]
Optimization and Affinity improvement
12	IgDiff	2024	De novo antibody design	Not Mentioned	[294]
13	AbGAN-LMG	2023	Higher-quality antibody libraries generation and optimization	https://github.com/Zhaowenbin98/AbGAN-LMG	[85]
14	Ens-Grad	2020	CDR design	https://github.com/gifford-lab/antibody-2019	[295]
15	OptMAVEn2.0	2018	De novo Design of Antibody Variable Region	https://github.com/maranasgroup/OptMAVEn_2.0	[141]
16	OptCDR	2010	CDR designing	http://maranas.che.psu.edu (link not working)	[80]
17	MEAN	2023	antibody design	https://github.com/THUNLP-MT/MEAN
Generating CDR Libraries
18	IgLM	2023	Generates full-length antibody sequences and Infilled CDR H3 loop libraries generated	https://github.com/Graylab/IgLM	[215]
19	reportBERT
Optimizing CDR Immunogenicity
20	EquiPocket	2023	Binding site prediction	Not Mentioned	[249]
21	AbAgIntPre	2022	Predict antibody-antigen interactions	http://www.zzdlab.com/AbAgIntPre/	[157]
22	DLAB	2022	Predict antibody–antigen binding for antigens/ binder/ Virtual screening/ non-binder classifier	https://github.com/oxpig/dlab-public	[296]
23	PECAN	2020	Predict binding interfaces on both antibodies and antigens	https://github.com/vamships/PECAN	[297]
Epitope and paratope prediction
24	Paragraph	2023	Antibody paratope prediction	https://github.com/oxpig/Paragraph	[298]
25	SEMA	2022	B-cell conformational epitope prediction	https://github.com/AIRI-Institute/SEMAi	[237]
26	EPMP	2021	Joint epitope-paratope prediction	NA	[299]
Miscellanies
27	AbSciBio	2024	De novo antibody design	https://github.com/AbSciBio/unlocking-de-novo-antibody-design	[142]
28	ProGen2	2023	Modeling evolutionary sequence distributions, creating novel sequences, and predicting protein fitness	https://github.com/salesforce/progen	[240]
29	Protpardelle	2023	Generative model for protein design	https://github.com/ProteinDesignLab/protpardelle	[300]
30	AbLang	2022	Restores the missing residues of antibody sequences	https://github.com/oxpig/AbLang	[246]
31	AbBERT-HMPN	2022	Generation of sequences and structures, focusing on the design of antigen-binding CDR-H3 regions	Not Mentioned	[210]
32	AntiBERTa	2022	Tracing B cell origins, quantifying immunogenicity, and predicting antibody binding sites	https://github.com/alchemab/antiberta	[198]
33	HERN (Hierarchical Equivariant Refinement Net- work)	2022	Antibody docking and design	https://github.com/wengong-jin/abdockgen	[301]
34	RoseTTAFold Diffusion (RFdiffusion)	2022	Enables the creation of complex, functional proteins from basic molecular conditions	https://github.com/RosettaCommons/RFdiffusion	[302]
35	AntiBERTy	2021	Understanding of immune repertoires/and affinity maturation/ insights into antigen binding	https://github.com/jeffreyruffolo/AntiBERTy	[241]
36	RefineGNN	2021	Optimization guided by specific properties to design new antibodies with enhanced neutralization capabilities	https://github.com/wengong-jin/RefineGNN	[250]
37	LSTM based study	2021 2022	Antibody design and affinity maturation Antibody Binding site prediction	Not Mentioned https://github.com/mpcrlab/AntibodyBindingPrediction	[226] [227]
38	Fold2Seq	2021	Designing protein sequences tailored to a specific target fold	https://github.com/IBM/fold2seq	[303]
39	UniRep	2019	Protein engineering and informatics	https://github.com/churchlab/UniRep	[304]

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ISSN: 2050-7771

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