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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5629_Библиотеки_им_академика_М_И_Перельмана.pdf
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- •Contents
- •Foreword
- •Preface
- •About the Editors
- •Contributors
- •References
- •2.3.4 Barriers to Automation Adoption
- •2.4 Core Ingredients for Successful Digital Transformation
- •2.1 Introduction
- •2.3.1 Operational Challenges
- •2.3.2 Cultural Challenges
- •2.4.2 Cloud Computing
- •2.5 Case Studies of Successful Digital Transformation
- •2.6 Conclusion
- •References
- •3. Computational Protein Design Strategies for Optimization of Antigen Generation to Drive Antibody Discovery
- •3.1 Introduction
- •3.3 Antigen Generation Strategies
- •3.4 Computational Methods
- •3.4.2 Computational Protein Structure Prediction
- •References
- •4. Bioinformatic Analyses of Antibody Repertoires and Their Roles in Modern Antibody Drug Discovery
- •4.1 Introduction
- •4.6 Summary and Future Directions
- •Acknowledgments
- •References
- •5.1 Introduction
- •5.2 Databases
- •5.2.1 Databases in Machine Learning Approaches
- •5.2.2 Database Types
- •5.3 Applications of Machine Learning in Antibody Discovery and Development
- •5.3.1 Structure Prediction with Deep Learning
- •5.3.3 Developability
- •5.4 Antibody Generation and Design by Language Models
- •5.4.1 Antibody Representations
- •5.4.2 Representation Learning
- •5.4.3 Language Models
- •References
- •6.1 Introduction
- •6.2 Antibody Generation through Deep Generative Models
- •6.3.1 Sampling and Scoring
- •6.5 Conclusions and Perspectives
- •Acknowledgments
- •References
- •7.1 Introduction
- •7.2.3 Computational Approaches to Predict Antibody–Antigen Interaction
- •7.3 Conclusion
- •Competing Interests
- •Acknowledgments
- •References
- •8.2 Common Types of Molecular Simulations for Biomolecules
- •8.2.1 Molecular Dynamics (MD) Simulations
- •8.2.2 Monte Carlo (MC) Simulations
- •8.2.3 Challenges of Molecular Simulations
- •8.3.1 Periodic Boundary Conditions
- •8.4 Uses of Molecular Simulation in Antibody Drug Development
- •8.5 Conclusion
- •References
- •9. Considerations of Developability During the Early Stages of Antibody Drug Discovery and Design
- •9.1 Introduction
- •9.2 Historical Perspective
- •9.3 Clinical Antibody Data Set
- •9.5 Control Antibodies
- •9.7 Assessment of Chemical Liabilities
- •9.8 Conclusions and Future Perspectives
- •Acknowledgments
- •References
- •Abbreviations
- •10.1 Introduction
- •10.4.1 Conclusions and Outlook
- •Acknowledgments
- •References
- •11.8 Conclusions and Future Directions
- •References
- •12.1 Introduction to PK/PD and QSP Modeling
- •12.1.1 PK/PD Modeling
- •12.1.2 QSP Modeling
- •12.2.1 Monoclonal Antibodies (mAbs)
- •12.2.3 Cell Therapies
- •12.2.4 Gene Therapies
- •12.2.5 Vaccines
- •12.2.6 mRNA/siRNA/Oligonucleotide Therapeutics
- •12.4 Case Studies
- •12.5 Conclusions and Future Perspectives
- •References
- •13.1 Introduction
- •13.2 AI/ML: A Game Changer for Antibody Design
- •13.3 Multispecific Antibody Design
- •13.4 Adapting AI to the Design of Multispecific Antibodies
- •13.4.1 Structure Prediction and Modeling
- •13.4.2 Developability Prediction and Optimization
- •13.4.4 In Silico Modeling and Simulation
- •13.5 The Future: Beyond Optimization
- •13.5.1 Market Trends and Commercialization
- •13.5.2 Logic Gates, Biosensors, and De Novo Design
- •13.5.3 Challenges and Opportunities
- •13.6 Conclusion
- •Acknowledgments
- •References
- •Index

TABLE5.1 Examples of different antibody database types
DATABASE NAME DATABASE TYPE DATABASE CONTENT DESCRIPTION ACCESS LINK REFERENCES
AbMiner Experimental
specic
AntiJen Experimental
specic
IEDB Experimental
specic
IgPdb Experimental
specic
PCLICK Experimental
specic
SKEMPI 2.0 Experimental
specic
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 identiers
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 etal. 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 etal. 2020)
https://cab-rep.c2b2.
columbia.edu/
http://www.abybank.org/
emblig/
http://research.
naturalantibody.com/
nanobodies
(Major etal.
2006)
(Toseland etal.
2005)
NA
(Nguyen etal.
2017)
(Jankauskaite
etal. 2019)
(Guo etal. 2019)
NA
(Deszyński etal.
2021)
(Continued)
5 • Articial Intelligence and Machine Learning 81

TABLE5.1 (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 Specic
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
specic
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 etal.
http://www.imgt.org/ (Lefranc etal.
https://tabs.craic.com/ NA
https://github.com/sarahsirin/
AB-Bind-Database
(Corrie etal.
2018)
(Olsen, Boyles
etal. 2022a;
Kovaltsuk etal.
2018)
(Krawczyk,
Buchanan, and
Marcatili 2021)
(Honegger and
Plückthun 2001)
2017)
1999)
(Sirin etal. 2016)
(Continued)
82 Biopharmaceutical Informatics

TABLE5.1 (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 specic B-cell epitopes
CoV-AbDab Target specic Published or patented binding antibodies
and nanobodies to coronaviruses
Non-redundant Nanobody
database
sdAb-DB Target specic Single-domain antibody repository
Thera-SAbDab Target specic WHO-recognized antibody-related
For each antibody database type, multiple sources are presented above with a short description and access link.
Target specic 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 etal.
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 etal.
2014)
(Ferdous and
Martin 2018)
(Saha etal.
2005)
(Raybould etal.
2021)
(Zavrtanik and
Hadži 2019)
2018)
(Raybould etal.
2020)
5 • Articial Intelligence and Machine Learning 83

84 Biopharmaceutical Informatics
5.2.2.3 Databases with domain‑specic information
Sequence and structural data can be further enriched with antibody‑specic experi‑
mental information. Data on epitopes targeted by antibodies can be easily downloaded
from the IEDB (Vita etal. 2015), which now links such data to epitope‑specic anti‑
body sequences. One of the key pieces of information characterizing antibody‑epitope
interactions is the binding afnity. There are other more specialized resources such as
Ab‑Bind (Sirin etal. 2016), which contains data on 1101mutations in 32 antibody com‑
plexes, and SKEMPI (Jankauskaite etal. 2019), which curates binding energy data for
available structures but is not limited to antibody information only (Norman etal. 2020).
There also exist resources that are specic to an antibody target (e.g., CoV‑ABDAB)
(Raybould etal. 2021), application (e.g., therapeutics) (Raybould etal. 2020), or format
(e.g., nanobodies) (Deszyński etal. 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 etal. 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 etal. 1999). A single source of information sim‑
plies and shortens the time to arrive at a data point and streamlines data curation for
computational modeling (Deszyński etal. 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 etal. 2017). Dening the crystal structure of proteins poses many techni‑
cal challenges, generating signicant interest in methods for predicting the 3D coordi‑
nates from sequences (Kryshtafovych etal. 2021). There are only about 6,500 crystal

5 • Articial Intelligence and Machine Learning 85
structures of antibodies and their fragments (Fabs, Fcs, etc.), some of them in complex
with their antigen (Dunbar etal. 2014). This number recapitulates the natural structural
diversity surprisingly well (Krawczyk etal. 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 etal. 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 etal. 2021;
Kryshtafovych etal. 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 etal.
2015; Marks etal. 2011; Regep etal. 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 etal. 2022) demonstrated that CDRs have spe‑
cic 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 etal. 2022).
Antibody modeling methods build on deep learning architectures, devising solu‑
tions specic 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 Table5.2).
TABLE5.2 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 condence estimate for each of its
predictions
coordinates of the Cα atoms of the entire VH
domain
(Anand and
Huang 2018)
(Ruffolo etal.
2020)
(Ruffolo etal.
2022)
(Eguchi etal.
2022)
(Akpinaroglu
etal. 2022)
(Abanades
etal. 2022a)
(Cohen etal.
2022)
(Continued)

86 Biopharmaceutical Informatics
TABLE5.2 (Continued) Structural prediction models
METHOD METHOD DESCRIPTION REFERENCES
AbodyBuilder2 Deep learning model behind ABodyBuilder2 is an
antibody-specic version of the structure module in
AlphaFold-Multimer with several modications
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
etal. 2022b)
(Lee etal.
2022)
(Wu etal.
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 etal. 2014). The train‑
ing dataset included records from SAbDab (Dunbar etal. 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 etal. 2015) with quality in mind, including CDRH3loop 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 etal. 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 etal. 2021; Marks
etal. 2011; Källberg etal. 2012).
5.3.1.2 ABlooper
ABlooper proposed an alternative architecture for CDR prediction as Equivariant Graph
Neural Networks (Abanades etal. 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 condence was the agreement of these
ve networks on the generated coordinates. The benet 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 • Articial Intelligence and Machine Learning 87
5.3.1.3 DeepAb
Predicting CDR‑H3loops is a challenging task driven by the broader goal of reconstruct‑
ing the entire antibody variable region. Built on top of the DeepH3method, 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 etal. 2018).
This feature extraction enabled implicitly capturing certain structural properties–for
example, recreating the PyIgClassify annotations (Adolf‑Bryfogle etal. 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 etal. 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 sufcient levels that allow them to be reliably used as substitutes for crys‑
tal structures, providing models at the speed and scale (Krawczyk etal. 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 identication
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 etal. 2020). Parapred (Liberis etal. 2018) pioneered deep learning usage in
antibody‑antigen interface prediction (specically, 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 etal. 2013),
antibody i‑Patch (Krawczyk etal. 2013), and PARATOME (Kunik etal. 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 etal. 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 etal. 2022) and a structure as input by Paragraph
(Chinery etal. 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
polyspecicity of different paratopes. Nevertheless, despite such radical simplication,
such methods have proven utility in their therapeutic applications–for example, in the
orthogonal identication of antigen‑specic antibodies (Richardson etal. 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 etal. 2021) argued that asymmetric treatment was required for
paratope and epitope predictors. They proposed neural message‑passing architectures
that aim toward specic paratope and epitope prediction aspects, achieving signicant
improvements on both tasks. Another interesting development in this space is ScanNet
(Tubiana etal. 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 • Articial Intelligence and Machine Learning 89
more plentiful data (Tubiana etal. 2022) do not achieve better performance by order of
magnitude compared to non‑ML methods developed close to a decade ago (Krawczyk
etal. 2014). Therefore, specically 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 etal. 2020). The increase in deep learning model usage
applies to scoring different docking poses for protein‑protein functions in general (Geng
etal. 2019; Renaud etal. 2021; Wang etal. 2020b). Due to the different interface statis‑
tics (Krawczyk etal. 2013), antibody‑antigen docking is a subproblem of protein dock‑
ing in general (Ambrosetti etal. 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 etal. 2003) by constraining the para‑
tope and proceeding to rescoring poses in an antibody‑specic fashion (Sircar and Gray
2010; Krawczyk etal. 2014). Deep learning for antibodies employed docking to address
virtual screening through rescoring ZDOCK poses in an antibody‑specic way (Chen
etal. 2003). The network in use was a deep convolutional network that classied 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 microuidics 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 afnity (Bachas et al. 2022) and specicity (Zhang
etal. 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 classica‑
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‑specic predictors requires signicant 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 etal. 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 etal. 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 HER2generation 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 specic 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‑specic 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, efcacy, and pharmacology features termed “developability” (Jain
etal. 2017). There are multiple self‑association, polyspecicity, 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 etal. 2019) or non‑deep learning
approaches–for instance, random forests (Obrezanova etal. 2015). Here, we focus on
two aspects, singling out deimmunization or immunogenicity prediction and generalis‑
tic models for developability prediction.
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