pubs.acs.

org/jcim Application Note

AREA-AFFINITY: A Web Server for Machine Learning-Based

Prediction of Protein−Protein and Antibody−Protein Antigen
Binding Affinities
Yong Xiao Yang, Jin Yan Huang, Pan Wang, and Bao Ting Zhu*

Cite This: J. Chem. Inf. Model. 2023, 63, 3230−3237 Read Online
See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles.

ACCESS Metrics & More Article Recommendations

ABSTRACT: Protein−Protein binding affinity reflects the bind-

ing strength between the binding partners. The prediction of
Downloaded via 37.255.235.126 on July 16, 2023 at 09:46:10 (UTC).

protein−protein binding affinity is important for elucidating

protein functions and also for designing protein-based therapeu-
tics. The geometric characteristics such as area (both interface and
surface areas) in the structure of a protein−protein complex play
an important role in determining protein−protein interactions and
their binding affinity. Here, we present a free web server for
academic use, AREA-AFFINITY, for prediction of protein−protein
or antibody−protein antigen binding affinity based on interface
and surface areas in the structure of a protein−protein complex.
AREA-AFFINITY implements 60 effective area-based protein−
protein affinity predictive models and 37 effective area-based models specific for antibody−protein antigen binding affinity
prediction developed in our recent studies. These models take into consideration the roles of interface and surface areas in binding
affinity by using areas classified according to different amino acid types with different biophysical nature. The models with the best
performances integrate machine learning methods such as neural network or random forest. These newly developed models have
superior or comparable performance compared to the commonly used existing methods. AREA-AFFINITY is available for free at:
https://affinity.cuhk.edu.cn/.

■ INTRODUCTION
Protein−Protein interactions are involved in nearly all biological
contacts and the percentages of different surface amino acid
types,16 and the contacts-based method was implemented as a
processes of various living systems.1,2 Since the structure of a web server, i.e., PRODIGY (PROtein binDIng enerGY).17 In
our recent work, the area-based protein−protein binding affinity
protein largely determines its functions, it is critically important
prediction methods were developed using different interface and
to study the structural determinants of protein−protein binding
surface areas present in the structure of a protein−protein
interactions such that we can gain a deeper understanding of
complex.18,19 The performances of the area-based methods were
their structural as well as functional properties. One of the
found to be superior or at least comparable to those of
important issues in characterizing protein−protein interaction is
PRODIGY17 and LISA (Local Interaction Signal Analysis),20
to reliably estimate the binding strength between the two
which are considered the best existing methods based on linear
interacting proteins, namely, their binding affinity.
and nonlinear models, respectively, for prediction of protein−
Structure-based protein−protein binding affinity prediction
protein binding affinity.
has been explored using different methods in the past several
In the past two decades, antibody molecules have been widely
decades.3−11 It is of note that several empirical functions for
used as protein therapeutics, which can recognize antigens with
protein−protein binding affinity prediction have been devel-
high affinity and specificity.21−23 It is important to accurately
oped in recent years.12−15 For example, the minimal model was
predict the antibody−antigen binding affinity for successful
constructed only using two variables: the interface area and the
square of root-mean-square displacement of the Cα atoms of the
interface residues upon binding;12 the minimalistic predictor Received: November 28, 2022
only employed the interface areas of different amino acid Published: May 26, 2023
types;14 the interface amino acid count model only used the
numbers of different interface amino acid types.15 Additionally,
the contacts-based method for binding affinity prediction was
developed using the numbers of different interface amino acid
© 2023 The Authors. Published by
American Chemical Society https://doi.org/10.1021/acs.jcim.2c01499
3230 J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling
antibody design. Affinity predictive models for general protein−
protein complexes often fail to achieve the same level of
performance in predicting the antibody−protein antigen
binding affinity.24 Certainly, more effective models are needed
for improved prediction of the binding affinities of the
antibody−protein antigen complexes. Recently, we have
constructed area-based affinity predictive models specific for
antibody−protein antigen complexes.19 The performances of
these area-based models are better than the performance of
CSM-AB, a graph-based antibody−antigen binding affinity
predictive model.25
In the present work, the area-based models developed in our
recent studies18 are implemented in the web server AREA-
AFFINITY, which is a free academic online tool for the
prediction of the binding affinities of the protein−protein or
antibody−protein antigen complexes based on three-dimen-
sional (3D) structures.
■ MATERIALS AND METHODS
Structures of the Complex. The input for AREA-
AFFINITY is the structure of the complex in the Protein Data
Bank (PDB) format. The structure of the protein−protein
complex or the antibody−protein antigen complex can be
retrieved from the Protein Data Bank26 using the PDB
identification (ID) given by the user or uploaded from the
user’s personal computer. If the structure file is in mmCIF
format, the users can use a program, BeEM (https://github.
com/kad-ecoli/BeEM) developed by Zhang,27 or a web server
(https://mmcif.pdbj.org/converter/index.php?l=en) provided
by Protein Data Bank Japan,28 to convert the mmCIF structure
file to PDB format. It is of note that the small ligand and water
molecules are not considered in the area-based models at the
present stage, which are removed from the PDB file before the
surface and interface areas are calculated.
Generally speaking, structures obtained from experimental
approaches such as X-ray crystallography and cryo-electron
microscopy (cryo-EM) have far higher accuracy than those
predicted using homology modeling and AlphaFold2.29 The
users are advised to use structures with the highest accuracy
possible.
Area-Based Descriptors. Different descriptors such as
areas and contacts have been employed to predict protein−
protein binding affinity.12,14−16,18,20 Both the area-based and
contacts-based methods take joint consideration of the interface
and surface in their contribution to the binding affinity of a
protein−protein complex.16,18 In our recent works, different
linear and nonlinear models based on area-based descriptors
have been developed to discover the effective equations to
predict the protein−protein18 as well as the antibody−protein
antigen binding affinity.19 It is of note that, based on our recent
study of area-based prediction methods,18 a single class of
descriptors can reflect, to a certain degree, the quantitative
energy−area relationship (E ∝ −Sx, here, E, S, x represent
energy, area, and power exponent, respectively) in the protein−
protein interactions.
The primary components of area-based descriptors are
calculated using Qcontact30 (area of interface residue pair) and
dr_sasa31 (solvent accessible surface area of atom) in our recent
studies.18 According to the physicochemical properties, the 20
amino acid types are categorized into four groups: basic AAs
(basic amino acids: HIS, ARG, and LYS), nonpolar AAs
(nonpolar, hydrophobic amino acids: ILE, PHE, LEU, TRP,
ALA, MET, PRO, and VAL), polar AAs (polar but uncharged
3231
pubs.acs.org/jcim Application Note
amino acids: CYS, ASN, GLY, SER, GLN, TYR, and THR), and
acidic AAs (acidic amino acids: ASP and GLU). The surface area
is classified into 8 kinds: RSA (Receptor Surface Area) of basic
AAs (A1), RSA of nonpolar AAs (A2), RSA of polar AAs (A3),
RSA of acidic AAs (A4), LSA (Ligand Surface Area) of basic AAs
(A5), LSA of nonpolar AAs (A6), LSA of polar AAs (A7), and
LSA of acidic AAs (A8). The interface area is divided into 10
kinds: basic AAs ∼ basic AAs (A9), nonpolar AAs ∼ nonpolar
AAs (A10), polar AAs ∼ polar AAs (A11), acidic AAs ∼ acidic AAs
(A12), basic AAs ∼ nonpolar AAs (A13), basic AAs ∼ polar AAs
(A14), basic AAs ∼ acidic AAs (A15), nonpolar AAs ∼ polar AAs
(A16), nonpolar AAs ∼ acidic AAs (A18). Additionally, the total
RSA (A19), total LSA (A20), and total interface area (A21) are also
employed to construct the nonlinear models with explicit
formations.18
Different Models for Prediction of Protein−Protein
and Antibody−Protein Antigen Binding Affinities. Three
types of models, i.e., linear, nonlinear, and mixed models, have
been trained, generated, or constructed by employing area-based
descriptors.18 Linear models are generated using linear
regression,32 nonlinear models are constructed using trial-and-
error methods or trained using neural network33,34 or random
forest,35,36 and mixed models are generated using linear
regression32 based on nonlinear models. Among a large number
of models, some representative ones with good performance for
protein−protein binding affinity prediction are selected for
general use in predicting various types of protein−protein
binding affinities,18 whereas some other models with good
performance for antibody−protein antigen binding affinity
prediction are selected for exclusive use in predicting the
antibody−protein antigen binding affinities only.19
■ RESULTS AND DISCUSSION
Procedures of Binding Affinity Prediction by AREA-
AFFINITY. The general procedure of the binding affinity
prediction is summarized in Figure 1. First, the structure of
Figure 1. A flowchart for the area-based binding affinity prediction,
i.e., the AREA-AFFINITY. For a given structure of the protein−protein
complex, AREA-AFFINITY will calculate the area-based descriptors in
the complex and predict the binding affinity according to pretrained
area-based models.
the protein−protein complex or antibody−protein antigen
complex with high reliability is obtained from the experimental
studies or by using structure prediction methods. Then, the 18
area-based descriptors in the complex are calculated based on
the structure. Finally, the binding affinity is predicted using the
area-based models (60 representative models for protein−
protein binding affinity prediction or 37 representative models
https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling pubs.acs.org/jcim Application Note

Figure 2. The performances of the representative area-based models implemented in the web server AREA-AFFINITY and some of the other
methods. A. Sixty area-based models, PRODIGY and LISA for protein−protein binding affinity prediction. The data is based on refs 18 and 20. B.
Thirty-seven area-based models and CSM-AB for antibody−protein antigen binding affinity prediction. The data is based on our earlier study.19

specific for antibody−protein antigen binding affinity predic-
tion).
Performances of the Representative Models. The web
server, i.e., AREA-AFFINITY, implements the 60 representative
area-based models for protein−protein binding affinity
prediction18 and the 37 representative area-based models
specific for antibody−protein antigen binding affinity predic-
tion.19 There are three types of models, i.e., linear models,
nonlinear models (constructed, neural network, or random
forest), and mixed models (linear combination of nonlinear
models) trained based on experimentally obtained structural
data. Among the different sets, each one is adopted as the
training set in turn.18,19 According to the performances in
different sets, representative protein−protein binding affinity
predictive models with good performances are selected,18 and
representative antibody−protein antigen binding affinity
predictive models with good performances are also similarly
selected.19
3232
In the 60 representative models that are intended for general
use in predicting the protein−protein binding affinities, the
number of adopted descriptors is from 1 to 18.18 Two subsets
containing 52 or 24 protein−protein complexes with reliable
experimental binding affinity values were used for testing. As
shown in Figure 2A, the best Pearson’s correlation coefficient
(R) between the predicted and experimental binding affinities
for these 60 models is 0.87 for the 52 complexes and 0.92 in
another subset containing 24 oligomers with reliable exper-
imental binding affinity values.18 The performances of the best
models are superior to those of PRODIGY16,17 and LISA20
(Figure 2A).
In the 37 representative models that are exclusively developed
for predicting antibody−protein antigen binding affinities, the
number of adopted descriptors is from 4 to 18.19 As shown in
Figure 2B, the maximum Pearson’s correlation coefficient (R)
for these models is 0.74 in a set composed of 262 antibody−
protein antigen complexes and 0.85 in a set composed of 33
https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling
antibody−protein antigen complexes.19 The performances of
these models are superior to those of CSM-AB25 (Figure 2B).
The Web Server and Its Usage. The AREA-AFFINITY
server is freely available online (https://affinity.cuhk.edu.cn/)
for any user without the need to register beforehand (Figure 3).
Figure 3. The interface of the web server AREA-AFFINITY. The first
page contains the title of the web server, a brief introduction, graphicial
abstract, and the box for the user to provide the input information, i.e.,
the structural information on the protein−protein complex, chain
identifers of the binding partners 1 and 2 in the structure.
The user is required to provide three types of basic information:
PDB ID of the complex or the structure of the protein−protein
complex in PDB format, the chain identifiers of the binding
partner 1 (or the antibody), and the chain identifiers of the
binding partner 2 (or the protein antigen). The structure of the
protein−protein complex or the antibody−protein antigen
complex can be retrieved from the Protein Data Bank26 using
the PDB ID given by the user or uploaded from the user’s
personal computer.
It should be noted that only one structural model with the
same chain identifier is permitted in the PDB file. The chain
identifiers of the two binding partners in the protein−protein
complex or in the antibody−protein antigen complex should be
typed into the corresponding positions on the web server
(Figure 4A or Figure 5A). After the basic identifiers are filled in
the correct positions, the user can click the button “RUN” to
start the computation process, which usually takes less than 60 s
to complete the computation, and the web server will display the
predicted binding affinities of 60 models for the protein−protein
3233
pubs.acs.org/jcim Application Note
binding affinity prediction18 or the predicted binding affinities of
37 models for the antibody−protein antigen binding affinity
prediction.19
In the protein−protein complex or antibody-protein antigen
complex, it is estimated that the structure of each binding
partner should contain no fewer than 25 amino acid residues.
For the protein−protein complex, the algorithm automatically
calculates the numbers of the residues of the two partners in the
complex structure, and the partner with more residues in the
structure is used as the receptor, while the other partner is used
as the ligand for the prediction of the binding affinity. Therefore,
it is not necessary for the users to calculate the total numbers of
residues contained in the two binding partners for protein−
protein binding affinity prediction. The users can use either
protein in the complex as binding partner 1 or 2. In the case that
the two partners have the same number of residues, the output
for the predicted affinity (based on a given model) is the
calculated mean value of the following two situations: (a)
partners 1 and 2 are used as receptor and ligand, respectively;
(b) partners 1 and 2 are used as ligand and receptor, respectively.
For the antibody−protein antigen complex, the antibody
structure should contain both the heavy and light chains with at
least 400 residues. The number of residues in the protein antigen
structure should not be higher than the number in the antibody
structure.
The binding affinity is represented as log(K), where K is the
dissociation constant or inhibition constant. The well-known
quantitative relationship ΔG = RT ln(K) can be used to calculate
the binding energy (ΔG) in the complex using the predicted
binding affinity log(K). In the equation, R, T, and K are the gas
constant, Kelvin temperature, and dissociation (or inhibition)
constant (i.e., Kd or Ki), respectively. The room temperature of
25 °C (298 K) or 300 K (27 °C) is usually adopted in the
calculation. According to the data from affinity benchmark,37 the
experimental binding energy ΔG (kcal/mol) is approximately
1.3639 × log(K). The web server will display the predicted
binding affinity log(K) and the binding energy ΔG.
Applications and Examples. Here, two examples are
shown to demonstrate how to use AREA-AFFINITY. The
procedures are as follows.
1. Type PDB ID or choose and upload the file of interest
from a personal computer. For example, the file name for a
protein−protein complex is 1de4.pdb, then you choose
the file (in PDB format) and upload it to the Web site
(Figure 4A); in the same way, if the file name for an
antibody−protein antigen complex is 1ahw.pdb, then you
choose this file and upload it (Figure 5A).
2. Type in the chain identifiers for the binding partner 1 (or
the antibody) and the binding partner 2 (or the protein
antigen). In the case of a protein−protein complex
(Figure 4A), if the chain identifiers in the binding partner
1 are labeled C and F, then type in C,F in the
corresponding box; similarly, if the chain identifiers in
the binding partner 2 are labeled A and B, then type in
A,B. The same procedures are also used for the antibody−
protein antigen complex (Figure 5A).
3. Click the button “RUN” (Figure 4A or Figure 5A) to start
the computation. Usually, it will take less than 60 s to
complete the requested job.
4. After the computation job is successfully completed, the
web server will jump to a new page and display the
predicted results. The predicted binding affinity for the
https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling pubs.acs.org/jcim Application Note

Figure 4. Application EXAMPLE 1, i.e., prediction of the protein−protein binding affinity using AREA-AFFINIGY. A. The input interface of AREA-
AFFINITY for predicting protein−protein binding affinity using the example 1ed4.pdb. B. Predicted binding affinities of 60 models for a protein−
protein complex 1ed4.pdb. The experimental binding affinity (log(K)) and energy (kcal/mol) in protein−protein complex 1ed4_CF:AB are
−7.167 491 087 and −9.78, respectively.

protein−protein complex (1de4.pdb) using the best
representative model is shown in Figure 4B, and the
predicted binding affinity using the best representative
model specific for antibody−protein antigen interactions
(1ahw.pdb) is shown in Figure 5B. All the predicted
affinities of 60 models for protein−protein binding affinity
prediction or 37 models for antibody−protein antigen
binding affinity prediction can be downloaded through a
link on the same page.
As examples, the user can also click the buttons “Load
Example” and “RUN” in order to print the same results as
shown in Figure 4B or Figure 5B.
The Proper Use and Interpretation of the Predicted
Binding Affinity Data. The 60 models for protein−protein
binding affinity prediction are composed of 12 linear models, 6
constructed nonlinear models, 5 mixed models based on
constructed nonlinear models, 11 generated nonlinear models,
5 mixed models based on generated nonlinear models, 18
nonlinear (neural network) models, and 3 mixed models based
3234
on neural network models.18 The 37 models specific for the
antibody−protein antigen binding affinity prediction contain 2
linear models, 3 constructed nonlinear models, 14 nonlinear
(neural network) models, 14 nonlinear (random forest) models,
1 mixed model based on random forest models, and 3 mixed
models based neural network models.19
It should be noted that the predicted binding affinities, i.e., the
log(K) value, of the total 97 models represent the relative values,
which are only used for reference. The user can select the
predicted value of an appropriate model according to its
simplicity and performance/effectiveness. Among the 97
models, the 3 mixed models (based on the neural network
models) for protein−protein interactions and the 4 mixed
models (based on the neural network or random forest models)
specific for antibody−protein antigen interactions are the ones
that have the best performances with the protein−protein
binding affinity data sets used in the previous work18 and the
antibody−antibody binding affinity data sets used in the
previous work,19 respectively. Therefore, these models are
recommended for predicting the unknown binding affinity of a
https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling pubs.acs.org/jcim Application Note

Figure 5. Application EXAMPLE 2, i.e., prediction of the antibody−protein antigen binding affinity using AREA-AFFINIGY. A. The input interface
of AREA-AFFINITY for predicting antibody−protein antigen binding affinity using the example 1ahw.pdb. B. Predicted binding affinities of 37 models
specific for an antibody−protein antigen complex 1ahw.pdb. The experimental binding affinity (log(K)) and energy (kcal/mol) in antibody-protein
antigen complex 1ahw_AB:C are −8.468 521 083 and −11.55, respectively.

protein−protein complex or an antibody−protein antigen
complex with known structures, respectively. Here, only one
predicted affinity (from the best representative model) is shown
on the results page. The best representative model for the
protein−protein binding affinity prediction is the Mixed Model
1 (based on neural network models), and the best representative
model for antibody−protein antigen binding affinity prediction
is the Mixed Model 3 (based on neural network models). If the
users have their own reliable experimental binding affinity data
set, the users can also compare the performances of all the 97
models and select the best model(s) to predict the binding
affinities of the complexes with unknown experimental binding
affinities. This approach is strongly recommended for those
users who have a sufficiently large number of reliable
experimental binding affinity data.
The Structure of the Complex for Area-Based Binding
Affinity Prediction. In principle, all forms of highly reliable
experimental or predicted structures of the protein−protein
complexes or antibody−protein antigen complexes would be
suitable for the area-based models for prediction of their
3235
respective binding affinities. Generally speaking, structures
obtained from experimental approaches such as X-ray
crystallography and cryo-electron microscopy have higher
accuracy than those predicted using homology modeling and
AlphaFold2.29 The users are advised to use the structures with
the highest accuracy possible. Our models were trained by
experimentally determining complex structures. While it is
almost certain that the accuracy of the structures would affect
the prediction accuracy, it merits future investigation as to the
relationship between the structural accuracy and the prediction
accuracy of the area-based models.
■ CONCLUSIONS
Accurate prediction of the protein−protein or antibody−
protein antigen binding affinities is of paramount importance
to the understanding of protein functions and also to the rational
design of protein-based therapeutics and antibodies. The AREA-
AFFINITY web server implements 60 area-based models for
protein−protein binding affinity prediction and 37 area-based
models specific for antibody−protein antigen binding affinity
https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling
prediction. These predictive methods have superior or
comparable performances compared with the presently used
methods. It is hoped that AREA-AFFINITY may inspire the
future development of new simpler and more effective methods
for accurate prediction of the binding affinities of protein−
protein and antibody−protein antigen complexes.
■ ASSOCIATED CONTENT
Data Availability Statement
All the data sets are freely available in the supplementary data
files contained in our recent two studies18,19 (10.1016/j.bpc.
2022.106762 and 10.1016/j.jmgm.2022.108364), which can
also be downloaded from the Methods page of the web server
(https://affinity.cuhk.edu.cn/methods.html). The predictive
models are available and implemented via a user-friendly
interface at https://affinity.cuhk.edu.cn/. For Web site
information, please contact Yong Xiao Yang (yangyongxiao@
cuhk.edu.cn) and Pan Wang (wangpan@cuhk.edu.cn).
■ AUTHOR INFORMATION
Corresponding Author
Bao Ting Zhu − Shenzhen Key Laboratory of Steroid Drug
Discovery and Development, School of Medicine, The Chinese
University of Hong Kong, Shenzhen, Guangdong 518172,
China; Shenzhen Bay Laboratory, Shenzhen 518055, China;
orcid.org/0000-0001-8791-8460; Phone: +086-755-
84273851; Email: BTZhu@CUHK.edu.cn
Authors
Yong Xiao Yang − Shenzhen Key Laboratory of Steroid Drug
Discovery and Development, School of Medicine, The Chinese
University of Hong Kong, Shenzhen, Guangdong 518172,
China
Jin Yan Huang − Shenzhen Key Laboratory of Steroid Drug
Discovery and Development, School of Medicine, The Chinese
University of Hong Kong, Shenzhen, Guangdong 518172,
China
Pan Wang − Shenzhen Key Laboratory of Steroid Drug
Discovery and Development, School of Medicine, The Chinese
University of Hong Kong, Shenzhen, Guangdong 518172,
China
Complete contact information is available at:
https://pubs.acs.org/10.1021/acs.jcim.2c01499
Notes
The authors declare no competing financial interest.
■ ACKNOWLEDGMENTS
This work is supported by research grants from Shenzhen Key
Laboratory of Steroid Drug Discovery and Development (No.
ZDSYS20190902093417963), Shenzhen Peacock Plan (No.
KQTD2016053117035204) and Shenzhen Bay Laboratory
(No. SZB2019062801007).
■ REFERENCES
(1) Acuner Ozbabacan, S. E.; Engin, H. B.; Gursoy, A.; Keskin, O.
Transient protein-protein interactions. Protein Eng. Des Sel 2011, 24,
635−48.
(2) Gromiha, M. M.; Yugandhar, K.; Jemimah, S. Protein-protein
interactions: scoring schemes and binding affinity. Curr. Opin Struct
Biol. 2017, 44, 31−38.
(3) Horton, N.; Lewis, M. Calculation of the Free-Energy of
Association for Protein Complexes. Protein Sci. 1992, 1, 169−181.
3236
pubs.acs.org/jcim Application Note
(4) Kortemme, T.; Baker, D. A simple physical model for binding
energy hot spots in protein-protein complexes. P Natl. Acad. Sci. USA
2002, 99, 14116−14121.
(5) Ma, X. H.; Wang, C. X.; Li, C. H.; Chen, W. Z. A fast empirical
approach to binding free energy calculations based on protein interface
information. Protein Eng. 2002, 15, 677−81.
(6) Su, Y.; Zhou, A.; Xia, X. F.; Li, W.; Sun, Z. R. Quantitative
prediction of protein-protein binding affinity with a potential of mean
force considering volume correction. Protein Sci. 2009, 18, 2550−2558.
(7) Audie, J.; Scarlata, S. A novel empirical free energy function that
explains and predicts protein-protein binding affinities. Biophys. Chem.
2007, 129, 198−211.
(8) Vreven, T.; Hwang, H.; Pierce, B. G.; Weng, Z. P. Prediction of
protein-protein binding free energies. Protein Sci. 2012, 21, 396−404.
(9) Kastritis, P. L.; Bonvin, A. M. On the binding affinity of
macromolecular interactions: daring to ask why proteins interact. J. R
Soc. Interface 2013, 10, 20120835.
(10) Yan, Z. Q.; Guo, L. Y.; Hu, L.; Wang, J. Specificity and affinity
quantification of protein-protein interactions. Bioinformatics 2013, 29,
1127−1133.
(11) Erijman, A.; Rosenthal, E.; Shifman, J. M. How Structure Defines
Affinity in Protein-Protein Interactions. PLoS One 2014, 9, e110085.
(12) Janin, J. A minimal model of protein-protein binding affinities.
Protein Sci. 2014, 23, 1813−1817.
(13) Kastritis, P. L.; Rodrigues, J. P. G. L. M.; Folkers, G. E.; Boelens,
R.; Bonvin, A. M. J. J. Proteins Feel More Than They See: Fine-Tuning
of Binding Affinity by Properties of the Non-Interacting Surface. J. Mol.
Biol. 2014, 426, 2632−2652.
(14) Choi, J. M.; Serohijos, A. W. R.; Murphy, S.; Lucarelli, D.;
Lofranco, L. L.; Feldman, A.; Shakhnovich, E. I. Minimalistic Predictor
of Protein Binding Energy: Contribution of Solvation Factor to Protein
Binding. Biophys. J. 2015, 108, 795−798.
(15) Smith, J. K.; Jiang, S. Y.; Pfaendtner, J. Redefining the Protein-
Protein Interface: Coarse Graining and Combinatorics for an Improved
Understanding of Amino Acid Contributions to the Protein-Protein
Binding Affinity. Langmuir 2017, 33, 11511−11517.
(16) Vangone, A.; Bonvin, A. M. Contacts-based prediction of binding
affinity in protein-protein complexes. Elife 2015, 4, e07454.
(17) Xue, L. C.; Rodrigues, J. P.; Kastritis, P. L.; Bonvin, A. M.;
Vangone, A. PRODIGY: a web server for predicting the binding affinity
of protein-protein complexes. Bioinformatics 2016, 32, 3676−3678.
(18) Yang, Y. X.; Wang, P.; Zhu, B. T. Importance of interface and
surface areas in protein-protein binding affinity prediction: A machine
learning analysis based on linear regression and artificial neural
network. Biophys. Chem. 2022, 283, 106762.
(19) Yang, Y. X.; Wang, P.; Zhu, B. T. Binding affinity prediction for
antibody−protein antigen complexes: A machine learning analysis
based on interface and surface areas. Journal of Molecular Graphics and
Modelling 2023, 118, 108364.
(20) Raucci, R.; Laine, E.; Carbone, A. Local Interaction Signal
Analysis Predicts Protein-Protein Binding Affinity. Structure 2018, 26,
905.
(21) Sela-Culang, I.; Kunik, V.; Ofran, Y. The structural basis of
antibody-antigen recognition. Front Immunol 2013, 4, 302.
(22) Peng, H. P.; Lee, K. H.; Jian, J. W.; Yang, A. S. Origins of
specificity and affinity in antibody-protein interactions. Proc. Natl. Acad.
Sci. U. S. A. 2014, 111, E2656−65.
(23) Robin, G.; Sato, Y.; Desplancq, D.; Rochel, N.; Weiss, E.;
Martineau, P. Restricted diversity of antigen binding residues of
antibodies revealed by computational alanine scanning of 227 antibody-
antigen complexes. J. Mol. Biol. 2014, 426, 3729−3743.
(24) Guest, J. D.; Vreven, T.; Zhou, J.; Moal, I.; Jeliazkov, J. R.; Gray, J.
J.; Weng, Z.; Pierce, B. G. An expanded benchmark for antibody-
antigen docking and affinity prediction reveals insights into antibody
recognition determinants. Structure 2021, 29, 606−621.
(25) Myung, Y.; Pires, D. E. V.; Ascher, D. B. CSM-AB: graph-based
antibody-antigen binding affinity prediction and docking scoring
function. Bioinformatics 2022, 38, 1141−1143, DOI: 10.1093/bio-
informatics/btab762.
https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237
Journal of Chemical Information and Modeling pubs.acs.org/jcim Application Note

(26) Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.
N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank.
Nucleic Acids Res. 2000, 28, 235−42.
(27) Zhang, C. BeEM: fast and faithful conversion of mmCIF format
structure files to PDB format. bioRxiv 2022, DOI: 10.1101/
2022.11.11.516190.
(28) Bekker, G.-J.; Yokochi, M.; Suzuki, H.; Ikegawa, Y.; Iwata, T.;
Kudou, T.; Yura, K.; Fujiwara, T.; Kawabata, T.; Kurisu, G. Protein
Data Bank Japan: Celebrating our 20th anniversary during a global
pandemic as the Asian hub of three dimensional macromolecular
structural data. Protein Sci. 2022, 31, 173−186.
(29) Jumper, J.; Evans, R.; Pritzel, A.; Green, T.; Figurnov, M.;
Ronneberger, O.; Tunyasuvunakool, K.; Bates, R.; Ž ídek, A.;
Potapenko, A.; Bridgland, A.; Meyer, C.; Kohl, S. A. A.; Ballard, A. J.;
Cowie, A.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Adler, J.; Back, T.;
Petersen, S.; Reiman, D.; Clancy, E.; Zielinski, M.; Steinegger, M.;
Pacholska, M.; Berghammer, T.; Bodenstein, S.; Silver, D.; Vinyals, O.;
Senior, A. W.; Kavukcuoglu, K.; Kohli, P.; Hassabis, D. Highly accurate
protein structure prediction with AlphaFold. Nature 2021, 596, 583−
589.
(30) Fischer, T. B.; Holmes, J. B.; Miller, I. R.; Parsons, J. R.; Tung, L.;
Hu, J. C.; Tsai, J. Assessing methods for identifying pair-wise atomic
contacts across binding interfaces. J. Struct Biol. 2006, 153, 103−12.
(31) Ribeiro, J.; Rios-Vera, C.; Melo, F.; Schuller, A. Calculation of
accurate interatomic contact surface areas for the quantitative analysis
of non-bonded molecular interactions. Bioinformatics 2019, 35, 3499−
3501.
(32) Nievergelt, Y. A tutorial history of least squares with applications
to astronomy and geodesy. J. Comput. Appl. Math 2000, 121, 37−72.
(33) Rumelhart, D. E.; Hinton, G. E.; Williams, R. J. Learning
Representations by Back-Propagating Errors. Nature 1986, 323, 533−
536.
(34) Li, J.; Cheng, J.-h.; Shi, J.-y.; Huang, F. Brief Introduction of Back
Propagation (BP) Neural Network Algorithm and Its Improvement. In
Advances in Computer Science and Information Engineering; Jin, D., Lin,
S., Eds.; Springer Berlin Heidelberg: Berlin, Germany, 2012; Vol. 169,
pp 553−558. DOI: 10.1007/978-3-642-30223-7_87
(35) Breiman, L. Random Forests. Machine Learning 2001, 45, 5−32.
(36) Breiman, L.; Friedman, J. H.; Olshen, R. A.; Stone, C. J.
Classification and Regression Trees; Routledge, 1984. DOI: 10.1201/
9781315139470
(37) Vreven, T.; Moal, I. H.; Vangone, A.; Pierce, B. G.; Kastritis, P. L.;
Torchala, M.; Chaleil, R.; Jimenez-Garcia, B.; Bates, P. A.; Fernandez-
Recio, J.; Bonvin, A. M.; Weng, Z. Updates to the Integrated Protein-
Protein Interaction Benchmarks: Docking Benchmark Version 5 and
Affinity Benchmark Version 2. J. Mol. Biol. 2015, 427, 3031−41.

3237 https://doi.org/10.1021/acs.jcim.2c01499
J. Chem. Inf. Model. 2023, 63, 3230−3237