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TABLE5.1 Examples of different antibody database types
DATABASE NAME DATABASE TYPE DATABASE CONTENT DESCRIPTION ACCESS LINK REFERENCES
AbMiner Experimental
specic
AntiJen Experimental
specic
IEDB Experimental
specic
IgPdb Experimental
specic
PCLICK Experimental
specic
SKEMPI 2.0 Experimental
specic
ABCD Sequence Manually curated depository of sequenced
cAb-Rep Sequence Curated human B-cell immunoglobulin
EMBLIg Sequence Antibody sequences automatically extracted
Integrated Nanobody
Database for Immunoinformatics (INDI)
Sequence Structure data and sequence information of
Matches commercially available antibodies to
their respective genomic identiers
Quantitative binding data for peptides
Experimental data on humans, non-human
primates, and other animal species antibody and T-cell epitopes
Inferred allelic variants for immunoglobulins
Antibody-antigen structures from a dataset
of antibody-antigen complexes using the CLICK method
Kinetics and energetics data upon mutation,
for protein-protein interactions including antibody-antigen complexes
antibodies
sequence repertoires
from EMBL-ENA
nanobodies created using an integrated curation approach from several sources
https://discover.nci.nih.gov/
abminer/
http://www.ddg-pharmfac.
net/antijen/AntiJen/ antijenhomepage.htm
https://www.iedb.org/ (Vita etal. 2015)
http://cgi.cse.unsw.edu.
au/~ihmmune/
http://mspc.bii.a-star.edu.sg/
minhn/cluster_pclick.html
https://life.bsc.es/pid/
skempi2/
https://web.expasy.org/abcd/ (Lima etal. 2020)
https://cab-rep.c2b2.
columbia.edu/
http://www.abybank.org/
emblig/
http://research.
naturalantibody.com/ nanobodies
(Major etal.
2006)
(Toseland etal.
2005)
NA
(Nguyen etal.
2017)
(Jankauskaite
etal. 2019)
(Guo etal. 2019)
NA
(Deszyński etal.
2021)
(Continued)
5 • Articial Intelligence and Machine Learning 81
TABLE5.1 (Continued) Examples of different antibody database types
DATABASE NAME DATABASE TYPE DATABASE CONTENT DESCRIPTION ACCESS LINK REFERENCES
iReceptor Sequence Antibody/B-cell and T-cell receptor repertoire
data from multiple independent repositories
OAS Sequence Annotated immune repertoires
Patented Antibody
Database
AAAAA Sequence/
abYsis Sequence/
IMGT Sequence/
Tabs–Therapeutic
Antibody Database
AB-Bind Specic
Sequence Sequence information found in patent
documents
Antibody receptor sequences and structures
Structure
Antibody sequence and structure data
Structure
Immunoglobulins, T-cell receptors, MHC, and
Structure
Sequence/
Structure/ Experimental specic
experimental
in the immunoglobulin and MH superfamilies, and related proteins of the immune system of vertebrates and invertebrates
Clinical trials, patents, papers, news, and
regulatory agencies
Contain experimental results for wild-type
and mutant antibodies and antigens
https://gateway.ireceptor.
org/
http://opig.stats.ox.ac.uk/
webapps/oas/
https://www.naturalantibody.
com/pad
https://plueckthun.bioc.uzh.
ch/antibody/
http://www.abysis.org/abysis/ (Swindells etal.
http://www.imgt.org/ (Lefranc etal.
https://tabs.craic.com/ NA
https://github.com/sarahsirin/
AB-Bind-Database
(Corrie etal.
2018)
(Olsen, Boyles
etal. 2022a; Kovaltsuk etal.
2018)
(Krawczyk,
Buchanan, and Marcatili 2021)
(Honegger and
Plückthun 2001)
2017)
1999)
(Sirin etal. 2016)
(Continued)
82 Biopharmaceutical Informatics
TABLE5.1 (Continued) Examples of different antibody database types
DATABASE NAME DATABASE TYPE DATABASE CONTENT DESCRIPTION ACCESS LINK REFERENCES
AbDb Structure Extracted from the PDB with standard
numbering schemes applied and redundancy information
SAbDab Structure Annotated antibody and nanobody
structures available in the PDB
SACS Structure Summary of antibody crystal structures in
the PDB
Bcipep Target specic B-cell epitopes
CoV-AbDab Target specic Published or patented binding antibodies
and nanobodies to coronaviruses
Non-redundant Nanobody
database
sdAb-DB Target specic Single-domain antibody repository
Thera-SAbDab Target specic WHO-recognized antibody-related
For each antibody database type, multiple sources are presented above with a short description and access link.
Target specic Non-redundant structures of nanobodies
therapeutics
http://www.abybank.org/
http://opig.stats.ox.ac.uk/
http://www.abybank.org/
https://webs.iiitd.edu.in/
http://opig.stats.ox.ac.uk/
https://www.sciencedirect.
http://www.sdab-db.ca/ (Wilton etal.
http://opig.stats.ox.ac.uk/
abdb/
webapps/sabdab
sacs/
raghava/bcipep/info.html
webapps/covabdab
com/science/article/pii/ S2352340919301052
webapps/newsabdab/ therasabdab/
(Ferdous and
Martin 2018)
(Dunbar etal.
2014)
(Ferdous and
Martin 2018)
(Saha etal.
2005)
(Raybould etal.
2021)
(Zavrtanik and
Hadži 2019)
2018)
(Raybould etal.
2020)
5 • Articial Intelligence and Machine Learning 83
84 Biopharmaceutical Informatics
5.2.2.3 Databases with domain‑specic information
Sequence and structural data can be further enriched with antibody‑specic experi‑ mental information. Data on epitopes targeted by antibodies can be easily downloaded from the IEDB (Vita etal. 2015), which now links such data to epitope‑specic anti‑ body sequences. One of the key pieces of information characterizing antibody‑epitope interactions is the binding afnity. There are other more specialized resources such as Ab‑Bind (Sirin etal. 2016), which contains data on 1101mutations in 32 antibody com‑ plexes, and SKEMPI (Jankauskaite etal. 2019), which curates binding energy data for available structures but is not limited to antibody information only (Norman etal. 2020). There also exist resources that are specic to an antibody target (e.g., CoV‑ABDAB) (Raybould etal. 2021), application (e.g., therapeutics) (Raybould etal. 2020), or format (e.g., nanobodies) (Deszyński etal. 2021).
5.2.2.4 Mixed databases
Some sources attempt to consolidate sequence and structure data. One example is abYsis, a web‑based antibody research system that contains both types of informa‑ tion (Swindells etal. 2017). Another example is the IMGT, a sequence, genomic, and structural knowledge resource dedicated to immunoglobulins, T‑cell receptors, MHC, the immunoglobulin and MH superfamilies, and related proteins of the vertebrate and invertebrate immune systems (Lefranc etal. 1999). A single source of information sim‑ plies and shortens the time to arrive at a data point and streamlines data curation for computational modeling (Deszyński etal. 2021).

5.3 APPLICATIONS OF MACHINE LEARNING IN ANTIBODY DISCOVERY AND DEVELOPMENT

Recent developments in computational antibody engineering enabled by ML and its subset, deep learning, have led to improvements in the previous state‑of‑the‑art methods such as structure prediction, binding prediction, and developability prediction. This sec‑ tion explores how deep learning has transformed the solutions to the previous antibody problems.

5.3.1 Structure Prediction with Deep Learning

Antibody structure prediction has a broad range of applications in antibody engineer‑ ing since the molecular shape of the paratope determines antibody‑antigen recognition (Kovaltsuk etal. 2017). Dening the crystal structure of proteins poses many techni‑ cal challenges, generating signicant interest in methods for predicting the 3D coordi‑ nates from sequences (Kryshtafovych etal. 2021). There are only about 6,500 crystal
5 • Articial Intelligence and Machine Learning 85
structures of antibodies and their fragments (Fabs, Fcs, etc.), some of them in complex with their antigen (Dunbar etal. 2014). This number recapitulates the natural structural diversity surprisingly well (Krawczyk etal. 2018), though inferring the structure of CDR‑H3 from its sequence remains a challenge.
The need to represent millions of possible antibody structures was traditionally addressed using homology modeling and energy‑based methods (Wilman etal. 2022). Such methods started ceding a way to deep learning methods, partly because of the solution to the general protein folding demonstrated by AlphaFold2 (Jumper etal. 2021; Kryshtafovych etal. 2021). Such protein structure prediction methods use data from coevolutionary signals, while this type of information is unavailable for antibodies. Paratope prediction and CDR‑H3, in particular, are particularly elusive (Jones etal. 2015; Marks etal. 2011; Regep etal. 2017). The original work of Chothia and colleagues (Chothia and Lesk 1987) and much later work (Adolf‑Bryfogle et al. 2015; North, Lehmann, and Dunbrack 2011; Kelow etal. 2022) demonstrated that CDRs have spe‑ cic clusters of conformations. Incorporating such classical papers into the development of ML methods may potentially improve the accuracy of antibody structure prediction, though in some cases, ML models implicitly infer such properties (Ruffolo etal. 2022).
Antibody modeling methods build on deep learning architectures, devising solu‑ tions specic to this class of molecules. In what follows, we highlight four of the avail‑ able recent methods that tackle the problem of antibody structure prediction (all methods are given in Table5.2).
TABLE5.2 Structural prediction models
METHOD METHOD DESCRIPTION REFERENCES
Generative
Modeling for Protein Structures
DeepH3 Model predicting the inter-residue distances and
DeepAb Deep residual convolutional network predicting bins
IG-VAE Variational autoencoder generating the 3D
DeepSCAb Model predicting inter-residue geometries as well as
Ablooper Model predicting the structure of CDR loops and
Nanonet Model given a sequence directly produces the 3D
Generative model predicting completions of
corrupted protein structures
orientations into a discrete set of bins, which is then used to score poses generated by RosettaAntibody
of distances and orientation angles, with a Rosetta-based protocol that realizes the structure of the predicted distance and angle constraints
coordinates of immunoglobulins
side-chain dihedrals of the antibody variable fragment
provides a condence estimate for each of its predictions
coordinates of the Cα atoms of the entire VH domain
(Anand and
Huang 2018)
(Ruffolo etal.
2020)
(Ruffolo etal.
2022)
(Eguchi etal.
2022)
(Akpinaroglu
etal. 2022)
(Abanades
etal. 2022a)
(Cohen etal.
2022)
(Continued)
86 Biopharmaceutical Informatics
TABLE5.2 (Continued) Structural prediction models
METHOD METHOD DESCRIPTION REFERENCES
AbodyBuilder2 Deep learning model behind ABodyBuilder2 is an
antibody-specic version of the structure module in AlphaFold-Multimer with several modications
EquiFold Model relies on geometrical structure, uses a novel
coarse-grained representation of protein structures that do not require multiple sequence alignments or protein language model embeddings
T-FoldAb Model generating simultaneous prediction of
backbone and side-chain conformations
xTrimoABFold Model predicts antibody structure from antibody
sequence based on a pre-trained antibody language model and homologous templates
A short description and reference are presented above for each structural prediction method.
(Abanades
etal. 2022b)
(Lee etal.
2022)
(Wu etal.
2022)
(Anonymous
2022)
5. 3.1.1 DeepH3
Based on RaptorX (Källberg et al. 2012), DeepH3 is a deep residual network used for de novo CDRH3 prediction. When given a one‑hot encoding, DeepH3 predicts the inter‑residue distances and orientations into a discrete set of bins, which is then used to score poses generated by RosettaAntibody (Weitzner etal. 2014). The train‑ ing dataset included records from SAbDab (Dunbar etal. 2014), with 99% sequence identity and thresholds and 3.0 Å resolution. The benchmark dataset used was based on 49 variable fragment (Fv) structures chosen from the PyIgClassify database (Adolf‑Bryfogle etal. 2015) with quality in mind, including CDRH3loop of lengths between 9 and 20 residues. The method achieves accuracies in the 2 Å region rather than the 4 Å in trRosetta, a solution designed for general protein structure prediction (Du etal. 2021). DeepH3 revealed that the distributions of orientation angles nd bet‑ ter use as discriminators than distance distributions alone, which were used in many previous methods for general protein structure prediction (Jumper etal. 2021; Marks etal. 2011; Källberg etal. 2012).
5.3.1.2 ABlooper
ABlooper proposed an alternative architecture for CDR prediction as Equivariant Graph Neural Networks (Abanades etal. 2022a). The solution encodes input data from SAbDab into 41‑dimensional vectors with amino acid type, atom type, and loop to which the residue belongs. Moreover, it gives sinusoidal positional embeddings to each residue to describe how close it is located to the anchors. SAbDab data were used to train ve E(G) NNs, each containing four layers. The prediction condence was the agreement of these ve networks on the generated coordinates. The benet of its method is its speed, as it does not rely on other structure generation algorithms and is capable of rapid generation of coordinates, given a framework structure from homology modeling.
5 • Articial Intelligence and Machine Learning 87
5.3.1.3 DeepAb
Predicting CDR‑H3loops is a challenging task driven by the broader goal of reconstruct‑ ing the entire antibody variable region. Built on top of the DeepH3method, DeepAb was designed to predict the whole variable regions. The method includes two main stages: (1) a deep residual convolutional network that predicts bins of distances and orienta‑ tion angles and (2) a Rosetta‑based protocol that realizes the structure of the predicted distance and angle constraints. Apart from the structural information given as input, the network includes a bidirectional‑long‑short term memory (LSTM) network trained on a set of 118,386 paired heavy and light chain sequences from OAS, with the goal of teaching the network the general features of antibody sequences (Kovaltsuk etal. 2018). This feature extraction enabled implicitly capturing certain structural properties–for example, recreating the PyIgClassify annotations (Adolf‑Bryfogle etal. 2015). The net‑ work also tracks residues contributing to the coordinate/angle prediction of each other using an attention mechanism. The model primarily attends to residues surrounding each loop analyzed, with the difference that CDRH3 predictions generate results from a broader set of dependencies across heavy and light chains.
5. 3.1.4 N anoNet
Methods such as DeepAb show the potential of ML techniques in antibody structural predictions. However, they may be hindered by slower methods required for generating coordinates. NanoNet addressed this issue (Cohen etal. 2022). The residual convolu‑ tional network was originally designed to predict structures of single‑chain nanobodies but could also be used for mAb chain structure prediction; it generates predicted alpha carbon coordinates as output when fed a one‑hot‑encoded variable region sequence. It aligns the input structures with developing a single frame of reference for the gener‑ ated predictions. Since the structure realization is carried out within a single network, NanoNet can produce thousands of structures in a few seconds.
The methods discussed above have enabled a dramatic improvement in the accu‑ racy of antibody structure prediction, achieving CDRH3‑level accuracy in the region of 2–3 Å rather than 3–4 Å previously (Almagro et al. 2014). These predictions are approaching sufcient levels that allow them to be reliably used as substitutes for crys‑ tal structures, providing models at the speed and scale (Krawczyk etal. 2018) required to address the antibody‑binding problem for the virtual screening of drug candidates.
5.3.2 Antibody‑Binding Prediction by Deep
Learning (Paratope Prediction)
Three‑dimensional structures of both antibodies and antigens play a key role in deter‑ mining antibody‑antigen interactions. Computational methods such as homology mod‑ eling, docking, and interface prediction can be employed during the lead identication and optimization phases to generate 3D models of antibodies and predict or identify the key residues that are part of antigen binding.
88 Biopharmaceutical Informatics
The development of novel binders was typically limited to animal immunizations of phage‑display methods. The methods for analyzing antibody‑antigen interactions were previously categorized into paratope, epitope, or docking, as reviewed previously (Norman etal. 2020). Parapred (Liberis etal. 2018) pioneered deep learning usage in antibody‑antigen interface prediction (specically, paratopes). However, the current combination of NGS and ML approaches opens the door to novel applications going beyond these three categories.
5.3.2.1 Paratope prediction
Solutions to paratope prediction were rst proposed by proABC (Olimpieri etal. 2013), antibody i‑Patch (Krawczyk etal. 2013), and PARATOME (Kunik etal. 2012). These methods relied on structural information and were based on statistical scores. Recently, the paratope prediction problem was addressed by deep learning methods that, surpris‑ ingly, do not even consider the structure.
Liberis and colleagues (Liberis etal. 2018) presented Parapred, a sequence‑based probabilistic ML algorithm for paratope prediction. The method improved on the current state‑of‑the‑art methodology and only required a stretch of the amino acid sequence corresponding to a hypervariable region as an input. No information about the antigen was required. Liberis and colleagues showed that such predictions could be used to improve both the speed and the accuracy of a rigid docking algorithm. Since then, the proposed improvements to paratope prediction employed ne‑tuning a lan‑ guage model via AntiBerta (Leem etal. 2022) and a structure as input by Paragraph (Chinery etal. 2022).
Within paratope prediction, one needs to keep in mind that most methods do not perform the predictions with respect to the antigen, which does not consider the possible polyspecicity of different paratopes. Nevertheless, despite such radical simplication, such methods have proven utility in their therapeutic applications–for example, in the orthogonal identication of antigen‑specic antibodies (Richardson etal. 2021).
5.3.2.2 Epitope prediction
The prediction of the paratope and epitope–the binding sites in antibody‑antigen inter‑ actions–is essential for vaccine and synthetic antibody development. Del Vecchio and colleagues (Del Vecchio etal. 2021) argued that asymmetric treatment was required for paratope and epitope predictors. They proposed neural message‑passing architectures that aim toward specic paratope and epitope prediction aspects, achieving signicant improvements on both tasks. Another interesting development in this space is ScanNet (Tubiana etal. 2022), an end‑to‑end, interpretable geometric deep learning model capa‑ ble of learning features directly from 3D structures. The model builds representations of atoms and amino acids using the spatio‑chemical arrangement of their neighbors. Tubiana and colleagues trained the model for detecting protein‑protein and protein‑anti‑ body‑binding sites, demonstrating its accuracy.
Though representing state of the art, the methods do not achieve quality comparable to experimental epitope mapping experiments. Notably, deep learning methods that use
5 • Articial Intelligence and Machine Learning 89
more plentiful data (Tubiana etal. 2022) do not achieve better performance by order of magnitude compared to non‑ML methods developed close to a decade ago (Krawczyk etal. 2014). Therefore, specically in the eld of epitope prediction, many issues still need to be addressed to reliably replace experimental epitope mapping methods.
5.3.2.3 Docking
A key application of predicting antibody‑antigen interactions is allowing researchers to leverage the large volume of NGS data to mine for novel binders (virtual screen‑ ing). Virtual screening initiatives in the area of small molecules often come together with large‑scale docking (Maia etal. 2020). The increase in deep learning model usage applies to scoring different docking poses for protein‑protein functions in general (Geng etal. 2019; Renaud etal. 2021; Wang etal. 2020b). Due to the different interface statis‑ tics (Krawczyk etal. 2013), antibody‑antigen docking is a subproblem of protein dock‑ ing in general (Ambrosetti etal. 2020; Kilambi and Gray 2017).
Within the remit of antibody‑antigen docking, one focuses on generating poses by general‑purpose docker such as ZDOCK (Chen etal. 2003) by constraining the para‑ tope and proceeding to rescoring poses in an antibody‑specic fashion (Sircar and Gray 2010; Krawczyk etal. 2014). Deep learning for antibodies employed docking to address virtual screening through rescoring ZDOCK poses in an antibody‑specic way (Chen etal. 2003). The network in use was a deep convolutional network that classied docking poses into a bucket, showing an interval of the fraction of native reconstructed contacts. This method further demonstrated how such predictions could be employed in a special case of discriminating SARS‑COV‑2 binders via a mock virtual screening exercise.
5.3.2.4 Binding prediction from sequence
Advances in microuidics technologies and NGS contributed a vast amount of anti‑ body repertoire sequencing data, opening the door to new opportunities for deep learn‑ ing‑based applications. Combining experimental data with ML methods shows the possibility of predicting binding afnity (Bachas et al. 2022) and specicity (Zhang etal. 2022).
This is illustrated by the example of a study by Lim and colleagues (Lim et al.
2022). They started by encoding antibody light‑ and heavy‑chain CDR3s into antibody images. Next, they built and trained a convolutional neural network model to classify binders and non‑binders. To improve model interpretability, they performed in silico mutagenesis to identify CDR3 residues playing an important role in binder classica‑ tion. The team built generative deep learning models using GAN models to produce synthetic antibodies against PD‑1 and CTLA‑4. The models generated variable‑length CDR3 sequences resembling real‑world sequences, showing that deep learning methods can be used to mine and learn patterns in antibody sequences, uncovering insights about antibody engineering, optimization, and discovery.
Generating such target‑specic predictors requires signicant data generation by deep mutational scans. This might seem counterintuitive to the purpose of computa‑ tional methods that should not require lengthy and costly experimental runs. However, in
90 Biopharmaceutical Informatics
such cases, training the model on several thousand experimentally generated sequences opens the door toward generation/enumeration and subsequent binding prediction of millions of sequences. Therefore, such approaches open the doors toward practical com‑ putational scanning for binders in the entire antibody space rather than sampling small subsets of it, as is the case in most experimental approaches.
5.3.2.5 Simulated Ab–Ag binding data
Even though experimentally generated data on binding becomes more high‑through‑ put, it still falls short of covering all the possible antibody‑antigen interaction pairs. To overcome this hurdle, researchers tested this concept in silico using simulated Ab–Ag binding data (Akbar etal. 2022). This allowed them to also perform a theoretical study of a general “binding objective function” and address the problem of “learnability” of the Ab–Ag recognition. Akbar and colleagues trained the LSTM‑recurrent neural net‑ work (RNN) on CDR‑H3 that were apriori computationally associated with develop‑ ability data (Robert etal. 2021). The simulations included a wide range of physiological antibody‑binding parameters and enabled the 3D structure computation of synthetic antibody‑antigen binding. The network generated sequences that exceeded the develop‑ ability parameters of sequences on which the model was trained. RNN‑LSTM models were trained separately on binders as positive data and non‑binders as negative data, suggesting that the design of native‑like CDR‑H3 sequences is possible without negative examples. Also, accuracy is likely to be further improved with more training examples. This fact could potentially reduce the cost of generating training datasets, given that the HER2generation rate of the RNN was remarkably high despite only being trained on positive data. In addition, by delivering binders against this target for training, the network could generate specic binders against HER2. This demonstrated that antibody properties are, in principle, trainable on multiple modalities– binding and develop‑ ability. The ability of in silico generative frameworks to generate antigen‑specic and developable immune receptor sequences on a large scale and on demand is a critical feature for the rapid synthesis of antibodies.

5.3.3 Developability

Creating an antibody binder that exhibits therapeutic action is only part of the drug development requirements. Such a molecule must meet various biophysical, manufac‑ turability, safety, efcacy, and pharmacology features termed “developability” (Jain etal. 2017). There are multiple self‑association, polyspecicity, solubility, and immu‑ nogenicity assays, among others, that need to be performed to derisk the molecule and let it into clinical trials. To reduce the experimental burden, researchers attempted to solve this issue using statistical models (Raybould etal. 2019) or non‑deep learning approaches–for instance, random forests (Obrezanova etal. 2015). Here, we focus on two aspects, singling out deimmunization or immunogenicity prediction and generalis‑ tic models for developability prediction.