nature computational science

Article https://doi.org/10.1038/s43588-023-00511-5

Efficient and accurate large library ligand

docking with KarmaDock

Received: 20 March 2023 Xujun Zhang1,6, Odin Zhang1,6, Chao Shen1, Wanglin Qu1, Shicheng Chen1,
Hanqun Cao2, Yu Kang 1, Zhe Wang1, Ercheng Wang3, Jintu Zhang1,
Accepted: 8 August 2023
Yafeng Deng4, Furui Liu3, Tianyue Wang1, Hongyan Du1, Langcheng Wang5,
Published online: 21 September 2023 Peichen Pan 1 , Guangyong Chen 3 , Chang-Yu Hsieh 1 &
Tingjun Hou 1
Check for updates

Ligand docking is one of the core technologies in structure-based virtual

screening for drug discovery. However, conventional docking tools and
existing deep learning tools may suffer from limited performance in terms
of speed, pose quality and binding affinity accuracy. Here we propose
KarmaDock, a deep learning approach for ligand docking that integrates the
functions of docking acceleration, binding pose generation and correction,
and binding strength estimation. The three-stage model consists of the
following components: (1) encoders for the protein and ligand to learn the
representations of intramolecular interactions; (2) E(n) equivariant graph
neural networks with self-attention to update the ligand pose based on
both protein–ligand and intramolecular interactions, followed by post-
processing to ensure chemically plausible structures; (3) a mixture density
network for scoring the binding strength. KarmaDock was validated on four
benchmark datasets and tested in a real-world virtual screening project that
successfully identified experiment-validated active inhibitors of leukocyte
tyrosine kinase (LTK).

Ligand docking, one of the core tasks in structure-based virtual screen-
ing (VS), plays a key role in protein–ligand (PL) binding pose generation,
PL binding affinity prediction, PL binding pose selection and VS1. In
general, traditional docking programs such as AutoDock 42, AutoDock
Vina3, LeDock4, Glide5 and GOLD6 utilize heuristic search algorithms
to explore a range of possible ligand conformations and scoring func-
tions (SFs) with simplified terms for ligand pose selection and PL bind-
ing strength estimation. The simplification enhances their efficiency
in large-scale VS, but this comes at the cost of decreased accuracy.
With the increasing size of compound libraries (for example, ZINC20
(ref. 7), with over 230 million purchasable compounds), the need for
faster methods for ultra-large VS has led to the development of a range
of acceleration methods, such as QuickVina 2 (ref. 8) and AutoDock
GPU9, as well as deep learning (DL) technologies for predicting binding
affinity and generating binding poses.
Following the remarkable achievement of AlphaFold2 (ref. 10)
in predicting protein structures at the atomic level from protein
sequences, an increasing number of researchers have started apply-
ing DL algorithms to predict ligand conformations11–13 and PL binding
poses14–19. Unlike traditional ligand docking methods, predicting PL
conformations with DL algorithms (especially graph neural networks,
GNNs) can accelerate the docking process and improve docking accu-
racy. Instead of searching and scoring, DL-based pose generation mod-
els (PGMs) generate binding poses through one of three methods: (1)

1
Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou,
Zhejiang, China. 2Department of Mathematics, Chinese University of Hong Kong, Hong Kong, China. 3Zhejiang Lab, Hangzhou, Zhejiang, China.
4
Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou, Zhejiang, China. 5Department of Pathology, New York University Medical Center, New York,
NY, USA. 6These authors contributed equally: Xujun Zhang, Odin Zhang. e-mail: panpeichen@zju.edu.cn; gychen@zhejianglab.com;
kimhsieh@zju.edu.cn; tingjunhou@zju.edu.cn

Nature Computational Science | Volume 3 | September 2023 | 789–804 789

Article
predicting PL distance matrices and generating PL binding poses using
gradient decent (for example, TankBind17), (2) implementing E(n)
equivariant graph neural network20 (EGNN) layers to predict the move-
ments and directions of ligand atoms in each message-passing iteration
(for example, EquiBind15 and E3Bind14) and (3) utilizing denoising dif-
fusion probabilistic models21 to predict the translation, rotation and
torsion of the ligands, similar to traditional docking tools (for exam-
ple, DiffDock19). Methods (1) and (3) are both capable of generating
conformations with chemically plausible local structures, albeit with
limited efficiency. Conversely, models based on an EGNN demonstrate
superior speed, yet face challenges in producing conformations with
chemically plausible bond lengths and bond angles. Although these
DL models (except EquiBind) have achieved substantial improvement
in docking pose generation, they are most effective in the scenario of
blind docking, where the binding site (or pocket) of the PL complex is
unknown. However, in VS practices, where the binding site is usually
known or identified through experiments beforehand22,23, pocket-given
ligand docking is more frequently used, and traditional docking tools
are mainly designed for this purpose. To address this problem, Lig-
Pose18 was introduced as a pocket-guided method utilizing EGNN with
self-attention to generate PL binding poses and predict their binding
affinities. LigPose has achieved an impressively high docking success
rate and low scoring error with a max 265-time speedup compared to
traditional tools. However, unlike traditional docking methods, the
predicted ligand conformations may not conform to physical rules
for bond lengths and angles, as geometric constraints are not imposed
during atom movement prediction.
Despite the fact that docking algorithms can produce accept-
able docking conformations, the accuracy of binding affinity predic-
tion (also known as the compound–protein interaction, CPI) is often
unsatisfactory, and this has led to the development of deep learning
scoring functions (DLSFs) models using various DL algorithms. Among
DLSFs, RTMScore24 uses mixture density networks (MDNs) to learn
the distance distribution of each PL node and determine the bind-
ing strength as the sum of the probabilities of PL nodes, achieving
impressive screening power and docking power. Although DLSFs can
outperform traditional SFs in binding affinity prediction, their accu-
racy is largely determined by the quality of the ligand-binding poses.
In this Article we present a DL approach called KarmaDock for
pocket-guided ligand docking (Fig. 1a) that can generate binding poses
and predict binding strength with fast speed and high accuracy. The
KarmaDock framework implements GNN architectures consisting of
two encoders (graph transformer (GT)24 and geometric vector percep-
tron (GVP)25), an MDN block for scoring and an EGNN block for docking
(Fig. 1b and Methods). The innovations of this approach are as follows:
(1) the protein is characterized based on residues rather than atoms so
as to encode geometric features and reduce computational cost; (2)
the probability distribution of the minimum distance between each
protein and ligand node learned by the MDN block can introduce a
distance inductive bias to the shared encoders, thereby helping to
guide the learning of pose generation; (3) two encoders are designed
to receive the distance inductive bias and to learn intramolecular
interactions for proteins and ligands, respectively; (4) fully connected
interaction graphs combined with a self-attention-based EGNN are
implemented to enable fast docking; and (5) two post-processing
methods are employed to ensure that the generated conformations
are rational in terms of bond length and angles.
KarmaDock was evaluated on four benchmark datasets for ligand
docking (PDBBind version 2020 (ref. 26), APObind27, Comparative
Assessment of Scoring Functions 2016 (CASF 2016) (ref. 28) and DEKOIS
version 2.0 (ref. 29), for the tasks of pose generation, pose selection and
VS). It has also been applied to real-world VS based on the ChemDiv
and Specs databases for identifying leukocyte tyrosine kinase (LTK)
inhibitors. For pose generation, KarmaDock outperforms all the tradi-
tional docking tools in terms of accuracy and speed, generating ligand
Nature Computational Science | Volume 3 | September 2023 | 789–804
https://doi.org/10.1038/s43588-023-00511-5
poses with a docking success rate of 89.1% and a speed of 0.017 s per
complex, and reproducing most interaction modes. For pose selec-
tion, KarmaDock achieves a success rate of 95.6% and is ranked second
among all the methods. In terms of VS, where docking accuracy, speed
and binding strength are all important, KarmaDock shows an aver-
age enrichment factor of 23.4 and 16.3 on the CASF 2016 and DEKOIS
version 2.0 datasets, respectively, which is higher than that achieved
by the traditional docking tools. Furthermore, KarmaDock is able to
screen 1.77 million compounds in 8.4 h (57.1 days for AutoDock GPU) on
a single Tesla V100, and successfully discovers an experiment-validated
LTK inhibitor with sub-micro activity. These results demonstrate the
superior performance of KarmaDock and show it to be a promising
tool for ultra-large VS.
Results
Docking accuracy and speed as a PGM
In this section, five traditional docking tools (AutoDock GPU9, Glide SP5,
Glide XP30, GOLD6 and LeDock4) were chosen for comparison. GOLD
and LeDock were selected as they are considered to have the best dock-
ing power among commercial and non-commercial docking tools,
respectively, according to Wang’s31 assessment of ten classic docking
tools. Glide SP and XP were chosen for their robust and accurate dock-
ing capabilities. AutoDock GPU was included for a fair comparison of
speed on a single graphics processing unit (GPU) between traditional
docking tools and PGMs. In addition, six PGMs (KarmaDock, LigPose,
TankBind, E3Bind, EquiBind and DiffDock) were included in the per-
formance comparison across various test sets. It should be noted that
TankBind, E3Bind, EquiBind and DiffDock were primarily designed for
blind docking and were trained and evaluated using the dataset-split
method proposed by EquiBind. Accordingly, they cannot be directly
compared with KarmaDock. To ensure a fair comparison between Kar-
maDock and PGMs on the EquiBind-split dataset, TankBind was selected
as a representative model, and the true binding sites instead of the
P2Rank-predicted binding sites were used. The docking performance
was further evaluated under a pocket-given situation. Except for the
pocket-guided TankBind and KarmaDock, the performance of the other
PGMs was obtained from reports, as some models are not open-source
or have not released their training scripts.
As shown in Fig. 2 and Supplementary Table 1, KarmaDock outper-
formed all traditional docking tools, with a minimum improvement
of 14.9%/22.3% in success rate on the PDBBind refined/core sets and a
speedup ranging from 163.06 to 8,182.70 times. When compared with
PGMs, KarmaDock maintained its superiority in terms of speed, with an
increase ranging from 2.38 to 2,352.94 times. It should be noted that the
speed of LigPose could not be directly compared, as its source data are
not publicly available and there is no information on its computational
speed. Based on the maximum speedup of 265 times compared with
traditional tools (including Glide XP) reported by LigPose, KarmaDock
reached a maximum speedup of 8,182.70 times compared with Glide
XP, suggesting that KarmaDock is faster than LigPose. As for the suc-
cess rate evaluated on the PDBBind refined set, both KarmaDock and
LigPose were trained on the PDBBind general set by excluding the
refined set. LigPose (74.7%) slightly outperformed KarmaDock (71.7%).
Unlike LigPose and KarmaDock, which were trained on the PDB-
Bind general set by excluding the refined set, the KarmaDock Raw
model was trained on the PDBBind general set with more training
samples. Post-processing was then applied in KarmaDock FF and Kar-
maDock Aligned by FF and RDkit-conformation-alignment, respec-
tively, to fix any implausible local structures in the poses generated by
KarmaDock Raw. The docking accuracy, as measured by success rate,
on the PDBBind core set showed the following order: KarmaDock Raw
(89.1%) > KarmaDock FF (88.4%) > KarmaDock Aligned (82.5%) = Lig-
Pose (82.5%) > KarmaDock (76.8%). Although LigPose cannot be trained
on the PDBBind general set as the model is not open-sourced, the high
success rate of KarmaDock Raw proved its power to generate accurate
790
Article https://doi.org/10.1038/s43588-023-00511-5

Protein Ligand Before docking Docking After docking Complex

b Graph representation KarmaDock architecture Interaction graph construction

Coords

Node feature
Node 1
Recycle
GVP Node 2
x3
Edge feature
block Node ..

Node N

Updated MDN Score: EGNN

node feature block 110.1 block

Node feature Node 1

GT Node 2

Edge feature block Node .. Coords

Node N

Random
Coords
Transform

c Node i_(l+1)
Graph transformer (GT)
edge ij_(l+1)
d Geometric vector perceptrons (GVPs)

Sequence
Embedding
TPF…PAA: Scalar feature
Concat Wm+b σ
Node scalar
Concat
Wh2(SiLU) We2(SiLU) Node vector
ǁ•ǁ2 ǁ•ǁ2 σ
↑ ↓ ← →
↑ ↓
Wh1(norm) We1(norm) ↑ ↓ ← → GVP layer Vector feature
↑ ↓
↑ ↓ ← →
↑ ↓ ← → ↑ ↓ ← → ↑ ↓ ← → ↑ ↓ ← →
↑ ↓
Edge scalar GVP ↑ ↓ ← → Wh ↑ ↓ ← → Wµ ↑ ↓ ← → X ↑ ↓ ← →
module ↑ ↓ ← → ↑ ↓ ← → ↑ ↓ ← → ↑ ↓ ← →
Wh0 We0
↑ → ↓ → GVP layer ↓ →
↓ →
4 heads ↑ → ↓ →
Sum_j ↑ → ↓ →
↓ →

Edge vector GVP layer

Softmax_j ×
e Mixture density network (MDN)

× Coords Protein Ligand Feature Distance

π
Node 1 Node 1
Node 1
Node 1 Node 2
Node 2
Node 1 …
1
Node .. 2
Node 1 Node N σ 3
Node N
WQ WK WV WE Node 2 Node 1 Linear 4
5
Node 2 Node 2 layer 6
Node 1
7
Node 2 … µ 8
Node 2
… …
Norm Norm Node ..
9
Node N Node 1 10
Node N
Node N Node .. –40 –20 0 20 40 60
Aux.
Coords Node N Node N Distance between protein node and ligand node
Node i_l Node j_l Edge ij_l

f E(n) equivariant graph neural networks (EGNN) Node i_l

Node i_l 4 heads

WQ+bQ wij Graph
Concat Wg+bg
norm
Gate Node i_(l+1)
Node j_l WK+bk Kij ǁ•ǁ2 Softmaxj block
Node i_l’ Gate block
WV+bv αij
Coords i_l Leaky
Wij WX1+bX1 WX2+bX2
ReLU

Dij Linear Mij Wh+bh

Concat Coords i_l Coords i_(l+1)
Coords j_l block
Node i_(l+1)

Coords update block

Edge ij_l Coords i_(l+1) Scale ∆X
We+be Coords j_l
Edge ij_(l+1) ǁ•ǁ2
Coords update block

Fig. 1 | Workflow of KarmaDock. a, Visualization of the docking process of
KarmaDock (from left to right). b, KarmaDock: graph representation, interaction
graph construction and architecture. c, Architecture of the first multi-head
attention layer of the graph transformer (GT). d, Architectures of the input layer
and the gvp layer of geometric vector perceptrons (GVPs). e, Architecture of the
mixture density network (MDN). f, Architecture of the first E(n) equivariant graph
neural network (EGNN) layer. Wx and bx denote the learnable parameters from
linear layers; ⊙ represents the Hadamard product; ⊕ denotes element-wise
summation; ⊖ denotes element-wise subtraction; × denotes the dot product;
‖ ⋅ ‖2 represents the L2 norm; Concat denotes the concatenation operation;
Softmax_ j represents the softmax operation on all neighborhood nodes j of node
i; Sum_ j denotes the sum operation on all the neighborhood nodes j of node i. In
b, Norm represents batch normalization, and SiLU is a type of activate function.
In d, embedding represents the embedding layer implemented in PyTorch, σ
represents a typical activation function or None operation, which varies in the
different layers, and arrows on the vector features represent their directions. In e,
π represents the mixing coefficients, μ and σ denote the means and s.d. values of
the distributions, respectively, Aux represents the predicted bond types and
atom types of auxiliary tasks. In f, Linear Block calculates as in equation (46), and
Leaky ReLU is a type of activation function.

Nature Computational Science | Volume 3 | September 2023 | 789–804 791

Article https://doi.org/10.1038/s43588-023-00511-5

a 1.0 b 1.0

0.8 0.8

0.6 0.6
Proportion

Proportion
Tool
KarmaDock
0.4 0.4
KarmaDock raw
Tool KarmaDock FF
KarmaDock KarmaDock aligned
AutoDock GPU AutoDock GPU
0.2 Glide SP 0.2 Glide SP
Glide XP Glide XP
LeDock LeDock
GOLD GOLD
0 0
0 2 4 6 8 10 0 2 4 6 8 10
R.m.s.d. R.m.s.d.

c d 139.106
140
3
120

2
100
log10(time cost)

Time cost (s)

1 80

60
0

40

–1 23.798
20
7.938
2.772 3.988
–2 0.017
0
KarmaDock AutoDock GPU GOLD LeDock Glide SP Glide XP KarmaDock AutoDock GPU GOLD LeDock Glide SP Glide XP
Tool Tool

Fig. 2 | The accuracy and speed of KarmaDock. a,b, Plots of empirical (b). KarmaDock Raw/FF/Aligned were trained on the PDBBind general set, and
cumulative distribution functions, which describe the proportion of KarmaDock was trained on the PDBBind general by excluding the refined set. c,
observations falling below each unique r.m.s.d. value of the complexes docked Plot of log10 time cost distributions of the various models. d, Average time costs
by various models on the PDBBind refined set (a) and the PDBBind core set of the various models.

binding poses. As expected, although the post-processing improved
the rationality of the poses, it also decreased the success rate, which
can be attributed to the fact that the force-field optimization ignores
the PL interactions, and the occasionally occurring big error torsion
angles from the raw predicted binding poses may greatly deviate the
aligned RDkit conformations from the raw predicted binding poses as
well as from the ground truth.
Acccording to evaluations following the dataset-split approach
proposed by EquiBind, KarmaDock (56.2%) outperformed TankBind
(24.2%) with given pockets, and DiffDock demonstrated state-of-the-
art blind-docking performance among TankBind, E3Bind, EquiBind
and DiffDock. Furthermore, a comparative analysis was conducted to
evaluate the performance of KarmaDock and conventional docking
tools on the APObind core set. This set mimics real-world scenarios
where only apo-protein structures are readily accessible. The data in
Supplementary Table 2 show that KarmaDock surpasses all traditional
docking tools in terms of both accuracy and speed. Notably, it exhibits
a minimum success rate augmentation of 56.7%.
Given that KarmaDock is capable of accurately generating PL
binding poses, we sought to understand the interaction patterns that
the model considers to be important in forming stable binding poses.
We quantified the interaction patterns, composed of eight common
non-bond interactions (Supplementary Section 3) of the crystal PL
complexes and the binding conformations generated by KarmaDock
in the PDBBind core set, and calculated the overlap rate. As shown in
Supplementary Fig. 1, we found that KarmaDock can consider metal
interactions, π interactions and salt bridges as the most important for
forming binding poses. We also wondered whether KarmaDock could
be used to refine the binding poses generated by traditional tools
(Supplementary Section 4). The docking poses of the complexes in
the PDBBind core set docked by five traditional docking tools were fed
into KarmaDock to replace the randomly initialized conformation for
initialization. As shown in Supplementary Fig. 3, the refined binding
poses generated by KarmaDock have lower root-mean-square devia-
tions (r.m.s.d.) and higher success rates compared with those docked
by traditional docking programs. However, the success rate for poses
after refinement is lower than that directly docked by KarmaDock, sug-
gesting that KarmaDock is best used as a standalone docking model.
Impact of ligand flexibility and dataset-split
It is widely recognized that the number of heavy atoms and rotatable
bonds in a ligand (that is, the ligand flexibility) greatly affect the speed
and success rate of traditional docking programs31. In this section we
explore the impact of these factors on the performance of both Karma-
Dock and traditional docking tools. As KarmaDock models the docking
process without considering bond constraints, the impact of rotatable
bonds can partially represent the impact of heavy-atom numbers. As
shown in Fig. 3a,b, traditional docking tools took longer as the number
of heavy atoms and rotatable bonds increased. Among the traditional
tools, AutoDock GPU was the fastest, with time costs ranging from 0.139

Nature Computational Science | Volume 3 | September 2023 | 789–804 792

Article https://doi.org/10.1038/s43588-023-00511-5

a 4–6
b 1–2
20.0

7–9 3–4
10–12 5–6
17.5
13–15 7–8
16–18 9–10
19–21 11–12 15.0
22–24 13–14

Rotatable bond number range

25–27 15–16
28–30 17–18 12.5
Heavy atom range

31–33 19–20

Time cost (s)

34–36 21–22
37–39 23–24 10.0
40–42 25–26
43–45 27–28
46–48 29–30 7.5

49–51 31–32
52–54 33–34
55–57 35–36 5.0

58–60 37–38
61–63 39–40
2.5
64–66 41–42
67–69 43–44
70–72 47–48
0
KarmaDock AutoDock GPU GOLD LeDock Glide SP Glide XP KarmaDock AutoDock GPU GOLD LeDock Glide SP Glide XP

c 4–6
d 1.0
1–3
7–9
4–6
10–12
13–15 7–9
16–18 0.8
10–12
19–21
22–24 13–15

25–27
Rotatable bond number range 16–18
28–30
Heavy atom range

19–21 0.6
31–33

Success rate
34–36
22–24
37–39
25–27
40–42
43–45 28–30 0.4
46–48
31–33
49–51
52–54 34–36
55–57
37–39
58–60 0.2

61–63 40–42

64–66
43–45
67–69
70–72 46–48
0
KarmaDock Glide XP Glide SP GOLD LeDock AutoDock GPU KarmaDock Glide XP Glide SP GOLD LeDock AutoDock GPU

e 7–9
f 1.0

1–3
10–12

13–15 4–6

16–18 0.8

7–9
19–21
Rotatable bond number range

22–24
10–12
25–27
Heavy atom range

0.6

Success rate
28–30 13–15

31–33

34–36 16–18

0.4
37–39
19–21
40–42

43–45
22–24
46–48 0.2

49–51 34–36

64–66
37–39
67–69
0
KarmaDock Glide XP Glide SP GOLD LeDock AutoDock GPU KarmaDock Glide XP Glide SP GOLD LeDock AutoDock GPU
Tool Tool

Fig. 3 | The impacts of heavy atoms and rotatable bond numbers on docking (c) and rotatable bond number (d) on models’ docking accuracy, tested on the
speed and accuracy. a,b, Impact of heavy atoms (a) and rotatable bond number PDBBind refined set. e,f, Impact of heavy atoms (e) and rotatable bond number
(b) on models’ docking speed (seconds per complex). c,d, Impact of heavy atoms (f) on models’ docking accuracy, tested on the PDBBind core set.

to 157.111 s, while Glide XP was the slowest program, with time costs As illustrated in Fig. 3c–f, the performance of traditional docking
ranging from 9.456 to 956.257 s. As for KarmaDock, the flexibility of software on the PDBBind refined and core sets decreased as the number
ligands had a limited influence on docking speed, which was reasonable of heavy atoms and rotatable bonds in a molecule increased, which is
given the high efficiency of batch processing on GPUs. understandable, as the search space for ligand conformation expands

Nature Computational Science | Volume 3 | September 2023 | 789–804 793

Article
dramatically with more heavy atoms and rotatable bonds. Surprisingly,
KarmaDock demonstrated consistent docking accuracy, regardless
of the numbers of heavy atoms and rotatable bonds, suggesting its
insensitivity to the flexibility of ligands. This is in contrast to LigPose,
which has been reported to suffer with highly flexible molecules18. One
possible explanation for this discrepancy is that the MDN module in
KarmaDock introduces an inductive bias about the inter-node distance
distribution of PL without regard to ligand flexibility, which enables the
model to effectively dock highly flexible molecules into the pocket.
We also investigated the impacts of the different dataset-split
methods listed in Supplementary Table 3 (details are provided in Sup-
plementary Section 1) on model performance. MLSF_Split and EquiB-
ind_Split split the dataset based on protein family similarity and ligand
heavy-atom number, respectively, and LigPose_Split considers both
factors. As shown in Supplementary Table 1, KarmaDock evaluated
using MLSF_Split (that is, KarmaDock Raw) achieved a 12.3% improve-
ment in success rate compared with KarmaDock trained on the Lig-
Pose_Split training set and tested on the PDBBind core set, suggesting
that the larger the training set and the more similar the protein family
between the training set and test sets, the more accurate the model
is. However, when KarmaDock was evaluated using MLSF_Split and
EquiBind_Split, the success rate dropped substantially from 89.1% to
56.2%. Because KarmaDock is insensitive to the number of heavy atoms,
the decrease can be attributed to the lower protein family similarity
between the training and test sets. In summary, the size of the train-
ing set and the family similarity between the training and test sets
can dramatically impact the success rate of KarmaDock, whereas the
number of heavy atoms and rotatable bonds has a limited influence.
We therefore retained the MLSF_Split method to train KarmaDock in
the following studies.
Impact of post-processing on the rationality of the binding poses
A drawback of EGNN is that it ignores bond-angle and bond-length
restrictions during the prediction of atom movements, which may
result in chemically implausible bond lengths and angles. To address
this issue, three strategies (Supplementary Section 2) and two types of
post-processing (Post-processing section) are employed in KarmaDock.
Furthermore, a metric called the rational rate is proposed to measure
the ability of models to generate chemically plausible conformations
by calculating the ratio of rational conformations among all the gen-
erated poses. A predicted conformation is considered illegal if the
differences (errors) of bond length or angle between the predicted
and ground-truth conformation exceed a certain threshold, where the
angle is indirectly measured by the distance between the end atoms
of two-hop bonds.
Figure 4a presents the distributions of the errors in the bonds
and angles between the ground-truth conformations and the poses
generated by KarmaDock, KarmaDock FF and KarmaDock Aligned.
The ‘max error’ records the maximum difference in bonds and angles
between a predicted pose and the ground truth, and the ‘mean error’
computes the average difference. As expected, the maximum error
distribution is higher than the mean error distribution. The bond
error distributions are lower compared with the angle distributions,
which is reasonable, as the angle information is hard to encode for the
model to learn. Among the models, the errors decrease in the order
KarmaDock > KarmaDock FF > KarmaDock Aligned, suggesting that
post-processing is effective and that RDkit-conformation alignment
is better than FF optimization. This is understandable, because the
RDkit conformation used in the alignment is 100% rational, whereas
the FF-optimized conformation can occasionally be illegal if the opti-
mization does not converge. Figure 4b describes the rational rate (also
referred to as success rate) under various combinations of bond/angle,
mean/max error, and three distance thresholds (1.0, 1.5 and 2.0 Å). The
conclusions in Fig. 4b–d are similar to those previously mentioned.
It is surprising to find that KarmaDock reaches a very high rational
Nature Computational Science | Volume 3 | September 2023 | 789–804
https://doi.org/10.1038/s43588-023-00511-5
rate without post-processing, indicating that the distance encoding
and ligand–ligand (LL) interaction used in KarmaDock help generate
chemically plausible conformations. We also provide a visualization
of the ground-truth conformation, the directly generated conforma-
tion, and the post-processed conformations (Fig. 4e). We can see that
the bond lengths of the directly predicted conformation are almost
correct, but the bond angles are not, which can be further improved
by post-processing.
Docking power and screening power as a DLSF
As a ligand-docking tool, it is essential to not only generate binding
poses but also score the binding strength between the protein and
ligand based on the generated binding poses. KarmaDock utilizes
the MDN scoring module, which has been shown to have satisfactory
docking and screening power in RTMScore. Accordingly, we tested
KarmaDock as an SF on poses provided by the classic CASF 2016 data-
set. Compared with RTMScore, which has already demonstrated the
capabilities of MDN as a scoring function, we focused on evaluating the
performance in terms of docking power and screening power, which
are crucial features for VS. The results presented in Supplementary
Data 1 indicate that KarmaDock exhibits strong performance in both
docking power and screening power, ranking first among all the tested
ligand-docking tools. KarmaDock also outperformed the other res-
coring methods except for RTMScore. The superior performance of
KarmaDock suggests that it could be highly effective in pose selection
and actives enrichment, thus demonstrating its potential as a promis-
ing docking tool.
Screening power as a ligand-docking tool
In a real-world VS, a ligand-docking tool is required to accurately predict
both the PL binding poses and their binding strengths, which cannot
be achieved solely by DLSFs or PGMs without a scoring module. Kar-
maDock, a DL model for ligand docking, has demonstrated exceptional
performance as both a PGM and a SF. In this study we evaluated the
VS performance of KarmaDock along with five traditional docking
tools (Glide SP, GOLD, LeDock, Surflex32 and AutoDock Vina), a PGM
with a scoring module (TankBind) and a sequence-based model (SBM,
TransformerCPI version 1) for screening power assessment. An intro-
duction to SBMs is provided in Supplementary Section 5. The inclusion
of TransformerCPI in the evaluation aimed to evaluate whether Karma-
Dock can attain a comparable level of efficiency to that of SBMs, while
also surpassing SBMs in terms of screening power. The performance
of these models was evaluated on DEKOIS 2.0, a classic benchmark
usually used for testing the VS power of SFs. The proteins and ligands
were first preprocessed using Schrödinger33, and then the binding
poses were generated by Glide SP. The influence of binding poses on VS
power was explored, and Fig. 5a,b shows that the binding poses gener-
ated by KarmaDock generally result in a higher Boltzmann-enhanced
discrimination of the receiver operating characteristic (BED_ROC)34
than those generated by Glide SP and refined by KarmaDock, while
the poses generated by Glide SP achieved the lowest BED_ROC. Con-
sidering that the SFs used in scoring the three groups of poses were
the same, the screening power performance can reflect the binding
pose accuracy. Therefore, it can be concluded that using KarmaDock
to refine the binding conformations generated by traditional tools can
improve the quality of poses; however, these are less accurate than
the binding poses generated directly by KarmaDock. From the per-
spective of models, we can observe from Fig. 5c,d that the screening
power rank is as follows: KarmaDock FF > KarmaDock Raw > KarmaDock
Aligned > Glide SP > Surflex > LeDock > GOLD ChemPLP > AutoDock
Vina > TankBind > TransformerCPI. Four conclusions can be drawn from
this rank: (1) the FF optimization can improve the screening power of
KarmaDock, while the RDkit-conformation alignment decreases the
screening power of KarmaDock; (2) KarmaDock outperformed all the
selected traditional docking tools and TankBind and TransformerCPI,
794
 Article https://doi.org/10.1038/s43588-023-00511-5

a b 1.02
2.00 KarmaDock aligned
KarmaDock FF
KarmaDock raw 1.000 1.000 1.000 1.000 1.000
1.75 1.00 0.998
0.992 0.993

0.984

Rational rate (error ≤ 1.0)

1.50 0.980 0.981
0.98
1.25
Error

0.96
1.00

0.75
0.94

0.50
0.92 0.915
KarmaDock aligned
0.25
KarmaDock FF
KarmaDock raw
0 0.90
Bond mean error Bond max error Angle mean error Angle max error Bond mean error Bond max error Angle mean error Angle max error
Error type Error type
c 1.02 d 1.02

1.000 0.999 1.000 1.000 1.000 1.000 0.999 1.000 1.000 1.000 1.000 1.000 1.000 1.000 0.999 1.000
1.00 0.995 1.00 0.996 0.996
0.993 0.993
0.989
0.986

Rational rate (error ≤ 2.0)

Rational rate (error ≤ 1.5)

0.98 0.98

0.963
0.96 0.96

0.94 0.94

0.92 0.92
KarmaDock aligned KarmaDock aligned
KarmaDock FF KarmaDock FF
KarmaDock raw KarmaDock raw
0.90 0.90
Bond mean error Bond max error Angle mean error Angle max error Bond mean error Bond max error Angle mean error Angle max error
Error type Error type

e
0.5 2.4
2.2
2.5

O
N
S
C

Raw FF Aligned Crystallized

Fig. 4 | Impact of post-processing on the rationality of the binding poses. a,
Distributions of bond length (angle) mean (max) errors between crystallized
conformations and conformations generated by KarmaDock with various
post-processing (KarmaDock Raw, no post-processing; KarmaDock FF,
conformations are post-processed by force-field optimization; KarmaDock
Aligned, conformations are post-processed by RDkit-conformation-alignment).
b–d, Rational rates of conformations generated by KarmaDock Raw/FF/Aligned,
defined by the ratio of the number of conformations whose bond length (or bond
angle) mean errors (or max errors) are no bigger than 1.0 (b), 1.5 (c) and 2.0 Å (d),
respectively, to the number of total conformations. e, An example (PDB 4JSZ) of
fixing a bond angle error by post-processing, where the bond angle is evaluated
indirectly by the two-hop distance, the yellow dashes denote the distance, and
the numbers around the yellow dashes are the distance value. ‘Raw’, ‘FF’ and
‘Aligned’ denote conformations generated by KarmaDock Raw/FF/Aligned,
respectively, and ‘Crystallized’ represents the ground-truth ligand-binding
conformation with rational bond lengths and angles.

demonstrating its superiority and validity in VS; (3) TankBind and Experimental validation in a real-world VS
TransformerCPI ranked last, showing that models that predict binding In 2021, CLIP1-LTK fusion has been identified as an oncogenic driver
strength without considering binding conformations cannot achieve in non-small-cell lung cancer (NSCLC)35 and is regarded as a critical
good screening power; (4) KarmaDock outperformed TransformerCPI target for treating corresponding cancers. To demonstrate the practi-
in terms of screening power with similar speed, suggesting that Kar- cal significance of KarmaDock in VS, we performed a real-world VS on
maDock can replace the role of SBMs in ultra-large VS to rapidly filter the LTK target. As no experimentally determined three-dimensional
probably inactive compounds and retain other compounds for further (3D) structure is available in PDB, SWISS-MODEL36 was employed for
rescoring through accurate SFs or MM/PB(GB)SA. protein homology modeling and protein structure generation, and

Nature Computational Science | Volume 3 | September 2023 | 789–804 795

Article https://doi.org/10.1038/s43588-023-00511-5

a b Score only 0.443 KarmaDock aligned 16.780

1.0
Refined aligned 0.457 Refined raw 16.985

KarmaDock aligned 0.458 KarmaDock raw 16.989

0.8

Mode
Refined raw 0.491 KarmaDock FF 17.434

Refined FF 0.504 Refined FF 17.442

Metric value

0.6
KarmaDock raw 0.512 Refined aligned 17.637

KarmaDock FF 0.519 Score only 19.413

0.4
Mode
0 0.1 0.2 0.3 0.4 0.5 0 5 10 15 20
KarmaDock raw
KarmaDock FF BED_ROC EF_0.5%
0.2 KarmaDock aligned
Refined raw KarmaDock aligned 15.202 Score only 6.430
Refined FF
Refined aligned Refined aligned 15.437 KarmaDock aligned 7.281
0 Score only
KarmaDock raw 15.833 Refined aligned 7.540
BED_ROC ROC_AUC PR_AUC

Mode
Refined raw 15.849 Refined FF 8.589

Score only 15.986 Refined raw 8.613

Mode
KarmaDock raw Refined FF 16.286 KarmaDock raw 8.709
30 KarmaDock FF
KarmaDock aligned KarmaDock FF 16.294 KarmaDock FF 8.710
Refined raw
25 Refined FF 0 2.5 5.0 7.5 10.0 12.5 15.0 0 2 4 6 8
Refined aligned EF_1% EF_5%
Score only
Metric value

20
Score only 0.709 Score only 0.267

KarmaDock aligned 0.744 Refined aligned 0.299

15
Refined aligned 0.755 KarmaDock aligned 0.299

Mode
10 Refined raw 0.780 Refined raw 0.347

Refined FF 0.780 Refined FF 0.349

5
KarmaDock raw 0.782 KarmaDock raw 0.360

0 KarmaDock FF 0.783 KarmaDock FF 0.360

EF_0.5% EF_1% EF_5% 0 0.2 0.4 0.6 0.8 0 0.1 0.2 0.3

Metric ROC_AUC PR_AUC

c Tool
d TranformerCPI 0.065 TranformerCPI 1.736

1.0 KarmaDock FF TankBind 0.107 TankBind 2.831

KarmaDock raw
AutoDock vina 0.140 AutoDock vina 5.464
KarmaDock aligned
Glide@SP GOLD@ChemPLP 0.171 GOLD@ChemPLP 5.750
0.8 Surflex LeDock 0.186 LeDock 6.777
Tool

LeDock
Surflex 0.220 Surflex 8.365
GOLD@ChemPLP
Metric value

AutoDock vina Glide@SP 0.378 Glide@SP 13.628

0.6 TankBind KarmaDock aligned 0.458 KarmaDock aligned 16.780
TranformerCPI
KarmaDock raw 0.512 KarmaDock raw 16.989

KarmaDock FF 0.519 KarmaDock FF 17.434

0.4
0 0.1 0.2 0.3 0.4 0.5 0 5 10 15
BED_ROC EF_0.5%
0.2 TranformerCPI 1.789 TranformerCPI 1.555

TankBind 2.898 TankBind 2.364

AutoDock vina 4.513 AutoDock vina 2.824

0
GOLD@ChemPLP 5.364 GOLD@ChemPLP 3.348

LeDock 5.856 LeDock 3.647

Tool

BED_ROC ROC_AUC PR_AUC

Surflex 7.301 Surflex 4.000

40 Glide@SP 12.095 Glide@SP 6.260

Tool
KarmaDock FF KarmaDock aligned 15.202 KarmaDock aligned 7.281

35 KarmaDock raw KarmaDock raw 15.833 KarmaDock raw 8.709

KarmaDock aligned
Glide@SP KarmaDock FF 16.294 KarmaDock FF 8.710
30 Surflex 0 2.5 5.0 7.5 10.0 12.5 15.0 0 2 4 6 8
LeDock
GOLD@ChemPLP
EF_1% EF_5%
25
Metric value

AutoDock vina TranformerCPI 0.538 TranformerCPI 0.053

TankBind
20 TankBind 0.600 TankBind 0.082
TranformerCPI
AutoDock vina 0.633 AutoDock vina 0.083

15 GOLD@ChemPLP 0.647 GOLD@ChemPLP 0.097

LeDock 0.653 LeDock 0.112

Tool

10 Surflex 0.673 Surflex 0.128

Glide@SP 0.742 Glide@SP 0.237

5 KarmaDock aligned 0.744 KarmaDock aligned 0.299

KarmaDock raw 0.782 KarmaDock raw 0.360

0 KarmaDock FF 0.783 KarmaDock FF 0.360

EF_0.5% EF_1% EF_5% 0 0.2 0.4 0.6 0.8 0 0.1 0.2 0.3

Metric ROC_AUC PR_AUC

Fig. 5 | Screening power on DEKOIS. a,b, Distributions (a) and average values
(b) of six metrics (BED_ROC, ROC_AUC, PR_AUC, EF_0.5%, EF_1% and EF_5%;
Methods) that KarmaDock achieves based on conformations generated under
various modes, respectively. ‘Score only’ means the binding conformations
are generated by Glide@SP. Refined Raw/FF/Aligned indicate that the binding
poses generated by Glide@SP are redocked by KarmaDock Raw/FF/Aligned.
KarmaDock Raw/FF/Aligned denote the binding poses generated by KarmaDock
Raw/FF/Aligned. c,d, Distributions (c) and average values (d) of six metrics
achieved by the various models (KarmaDock Raw/FF/Aligned, Glide@SP, Surflex,
LeDock, GOLD@ChemPLP, AutoDock Vina, TankBind and TransformerCPI).

the anaplastic lymphoma kinase (ALK) structure (4CLI) with high
sequence similarities to LTK was utilized as the template structure.
The Specs and ChemDiv databases, which are widely used commercial
compound libraries containing over 1.77 million molecules, were used
for screening. KarmaDock efficiently generated the binding poses and
scored binding strength in just 8.4 h. The ligands with top predicted
scores were further analyzed by comparing their interaction modes
with those of the crystallized ALK PL binding conformation, and 25
ligands forming binding conformations with good interaction modes
were selected for experimental validation (VS workflow targeting LTK
section and Supplementary Table 4). Among the 25 tested compounds,
compound 23 (ChemDiv ID 8005-7327) showed a half-maximum inhibi-
tory concentration (IC50) value of 765.6 nM, indicating its potential as a
candidate for further drug design. The binding modes of the complexes

Nature Computational Science | Volume 3 | September 2023 | 789–804 796

Article https://doi.org/10.1038/s43588-023-00511-5

a b

ARG-1120

MET-1199
ASP-1270 ASN-648
MET-593
GLY-663
GLY-1269

GLU-1197 GLU-591

c
Hydrogen
bonds

HIS-518
Halogen
bonds

Aromatic
hydrogen
bonds

O C (crystal lorlatinib)

MET-593 N C (docked lorlatinib)

H C (compound 23)

C (protein)

d Inhibition of lorlatinib e Inhibition of drug 23

100 100

80 IC50 = 2.36 nM 80 IC50 = 765.6 nM

60 60
Inhibition (%)
Inhibition (%)

40 40

20 20

0 0
0.01 0.1 1 10 100 1,000 1 10 100 1,000 10,000 100,000
–20 Concentration (nM) –20 Concentration (nM)

Fig. 6 | VS with experimental validation targeting LTK. a, The binding
pose and interaction mode of the target ALK and compound lorlatinib (PDB
4CTB). b, Binding pose and interaction mode of the target LTK and compound
lorlatinib generated by KarmaDock (the protein structure of LTK is generated
by AlphaFold2). c, Binding pose and interaction mode of the target LTK
and compound 23 (ChemDiv ID 8005-7327) generated by KarmaDock. d,e,
Inhibition curves of lorlatinib (d) and compound 23 (e) (ChemDiv ID 8005-7327).
The inhibition of Ba/F3-CLIP1-LTK cells is shown as the mean ± s.d. of three
independent experiments.

consisting of the protein and compounds (lorlatinib and ChemDiv with GLU-1197, MET-1199 and ARG-1120, and halogen bonds with GLY-
ID 8005-7327) were visualized, along with similar crystallized ligand 1269 and ASP-1270. A similar interaction mode (Fig. 6b) was found in
compounds (Fig. 6a–c). Analysis of the binding conformation of ALK the binding of LTK to lorlatinib generated by KarmaDock (hydrogen
and lorlatinib (Fig. 6a) revealed that lorlatinib forms hydrogen bonds bonds with GLU-591 and MET-593, and halogen bonds with GLY-663 and

Nature Computational Science | Volume 3 | September 2023 | 789–804 797

Article
ASN-648), suggesting KarmaDock can generate accurate binding poses
of PL based on interactions. As shown in Fig. 6c, the selected compound
23 (ChemDiv ID 8005-7327) also formed a hydrogen bond with MET-593,
similar to the former two complexes, which contributed to LTK inhibi-
tion and suggested that KarmaDock considered the hydrogen bonds
between LTK and compounds to be essential. Furthermore, an aromatic
hydrogen bond existed between the aromatic H on the compound
and the O on HIS-518, further improving the binding strength. Further
design and optimization based on the structure of this compound could
be carried out to explore its potential as a drug candidate.
Discussion
In the present investigation we have introduced a DL model, coined
KarmaDock, that is adept at generating binding conformations and
predicting binding strength with remarkable accuracy and expeditious
processing. Endeavors were made to implement post-processing tech-
niques, such as FF optimization and RDkit-conformation alignment, as
corrective measures for the inaccuracies in bond lengths and angles
detected in the predicted ligand conformations.
Notably, these post-processing approaches did enhance confor-
mation rationality, albeit at the cost of a decrease in docking accuracy,
presenting a challenging task in striking a balance between the two.
A pragmatic resolution appears to be a hierarchical screening of the
compound library, where the screening process initially bypasses con-
formation rationality, followed by an FF optimization of the top-scoring
complexes. Further experimentation with in-depth experimental vali-
dation can serve to confirm this solution and broaden the application
scope of KarmaDock.
However, it is worth acknowledging the inherent limitations of
KarmaDock, which presents as a semi-flexible docking tool with a
blind eye towards protein structure variation. This attribute perhaps
explains the observable decrease in performance on APObind. Our
forward-looking strategy, therefore, is to incorporate protein structure
variability within the purview of KarmaDock, with an ultimate aim of
transforming it into a fully flexible docking tool.
Methods
Architecture overview
As depicted in Fig. 1b, the ligand is characterized as a 2D molecular
graph Gc, with atoms as nodes and covalent bonds as edges, which is
a common approach in GNN-based DLSFs. The protein is represented
as a 3D residue graph Gp, with residues as nodes and edges connect-
ing the top 30 nearest-neighbor nodes, which captures long-range
interactions better and has a lower computational cost than a graph
with atoms as nodes.
Instead of directly being input to downstream tasks, the ligand
graphs and protein graphs are encoded by a GT24 and GVPs25 to learn
intramolecular interactions and update node embeddings:
H1c, s = GT (Hc,0 s , Ec,0 s ) (1)
1
Hp, 0 0 0 0 0 especially when considering the large number of protein atoms. To
s = GVP (Sp, s , Hp, s , Hp, v , Ep, s , Ep, v ) (2)
where H and E represent node and edge features, respectively, S repre-
sents the residue type, and subscripts c, p, s and v denote compound,
protein, scalar and vector, respectively.
The node embeddings (H1c, s , H1p, s ) from the encoders and the node
coordinates (X1c, s , X1p, s ) of both the ligand and protein are combined to
form an interaction graph [Gp, c = (Hp, c, Ep, c, Xp, c)], which captures inter-
molecular interactions at both the residue–atom and atom–atom
scales.
In the process of binding pose generation, the ligand conforma-
tion, represented as the coordinates of the ligand nodes, is initially
generated by RDkit and randomly rotated and shifted around the
Nature Computational Science | Volume 3 | September 2023 | 789–804
https://doi.org/10.1038/s43588-023-00511-5
pocket center. The node embeddings and edge features are initialized
by a graph normalization and an MLP layer (equation (3)). The node
embeddings, edge embeddings and ligand atom positions are then
updated through the application of the EGNN block, which consists
of eight EGNN layers with self-attention, taking into account both PL
interactions and ligand–ligand interactions (equation (4)). Inspired
by AlphaFold2 and LigPose, a recycling strategy is employed to enable
the EGNN block to learn how to consistently refine the binding poses.
At the start of each recycling, the updated embeddings and the raw
embeddings will be well combined through a gate block equation
(equation (5)). After the EGNN block, two types of post-processing
can be implemented to ensure that the generated conformations are
rational in terms of bond length and angles:
0, 0
Hp, c = GraphNorm (Hc, s , Hp, s ) (3)
r, l r, l r, l l
r, l−1 r, l−1 r, l−1
Hp, c , Ep, c , Xp, c = EGNN_Layer (Hp, c , Ep, c , Xp, c ) (4)
r+1, 0
Fp, c
r, 8
= Gate_Block(Fp, 0, 0
c , Fp, c ) (5)
where H and E represent the embeddings of a node and edge, respec-
tively, F refers to embeddings in general, and p, c, r and l represent
protein, compound, the recycling index and the EGNN layer index,
respectively.
Given the node embeddings and positions, the binding strength
can be predicted through the MDN block:
μp, c , σp, c , πp, c , dp, c = MDN_Block(Hc,1 s , Xc,1 s , Hp,
1 1
s , Xp, s ) (6)
P C
Score = ∑ ∑ logP ((dp, c , | , hp , hc )) (7)
p=1 c=1
where H and X represent the node embeddings and positions, respec-
tively, p, c and s refer to protein node, compound node and scalar
feature, respectively, μp, c , σp, c , πp, c , dp, c represent the means, s.d. val-
ues, mixing coefficients and node distances, respectively, and score
represents the predicted docking score.
Graph representation
In the present study, ligands are characterized as undirected compound
graphs [Gc = (Hc, Ec, Xc)], with atoms as nodes and covalent bonds as
edges, using torch_geometric. The node features Hc and edge features
Ec are generated by RDkit and TorchDrug, as outlined in Supplementary
Table 5, and the node positions Xc represent atom coordinates.
To predict PL binding poses based on non-bond interactions, it
is necessary to form edges between protein nodes and ligand nodes
for the model to learn those interactions. However, fully connecting
protein nodes and ligand nodes can be computationally expensive,
address this, we propose using residues as nodes in the protein graph,
which can substantially reduce the numbers of nodes and edges in
the graph. Furthermore, residue graphs can encode the geometric
information of each residue and capture long-range interactions
between both residue–residue pairs and PL nodes, which is beneficial
for binding-pose prediction. We constructed a K-nearest-neighbor
(KNN) graph [Gp = (Hp, Ep, Xp)] with K equal to 30, where the nodes
are represented by residues and alpha carbon (CA) atom coordinates
are used as node positions Xp. As shown in Supplementary Table 6,
the node features and edge features contain not only scalar features
(Hp_s, Ep_s), but also vector features (Hp_v, Ep_v), which can be utilized
by GVP for intramolecular topology and geometric representation
learning.
798
Article https://doi.org/10.1038/s43588-023-00511-5

Graph transformer fv1l = Wv0

l
fvl (18)
As has been demonstrated to be effective for molecular graph repre-
sentation, GT implemented in RTMScore24 is used as the ligand encoder
l l l
for intramolecular interaction learning (Fig. 1c). The node feature fv2 = Wv1 fv1 (19)
hc_i ∈ Rdh ×1 for the ith node and edge feature ec_ij ∈ Rde ×1 for the edge
between node i and node j are first initialized to h0c_i and e0c_ij with d
Slv1 = ‖‖ fv1
l ‖
‖2 (row wise) (20)
dimensions by two linear layers, respectively:

h0c_i = Wh0 hc_i + b0h

Slv2 = ‖ fv2
l
‖ (row wise) (21)
2

e0c_ij = We0 ec_ij + b0e (8) l

fsv = Concat ( fsl , Slv1 ) (22)

where Wh0 ∈ Rd×dh, We0 ∈ Rd×de and b0h , b0e ∈ Rd . The initialized node and
f sl̂ = Wsv
l l
fsv + blsv (23)
edge embedding are then input to the graph transformer layer stacking
six times to output the final embeddings of nodes and edges. The lth
graph transformer layer updates node edge embeddings using message fsl+1 = σs (f sl̂ ) (24)
passing and a modified multi-head self-attention (MHA) mechanism,
as shown in the following equations:
fvl+1 = σv (Slv2 ) ⊙ fv2
l
(row wise multiplication) (25)
qk,
c_i
l
= WQk, l Norm (hlc_i ) (9)
l l l
where Wv0 ∈ Rdv1 ×dv0, Wv1 ∈ Rdv2 ×dv1, Wsv ∈ Rds1 ×(ds0 +dv1 ) are learnable param-
l
eters; fv1 ∈ R dv1 ×3 l
, fv2 ∈ Rdv2 ×3
, Sv1 ∈ R , Slv2 ∈ Rdv2, fsvl ∈ Rds0 +dv1, blsv ∈ Rds1 ,
l dv1
kc_k, jl = WKk, l Norm (hlc_ j ) (10) l
fŝ ∈ Rds1 , fv ∈ Rdv2 ×3 and fs ∈ Rds1 are results of equations; σs and σv
l+1 l+1

represent the activation functions. Before being input to gvp layers,

the sequence information is embedded by the Embedding layer and
vk, l
= WVk, l Norm (hlc_ j ) (11)
c_ j concated with other scalar node features:

hseq = Embedding (Sequence) (26)

ek, l
c_ij
= WEk, l Norm (elc_ij ) (12)

hs = Concat (hs0 , hseq ) (27)

k, l
qc_i ⋅ kc_k, jl
wk, l
c_ij
= Softmaxj∈N(i) (( k, l
) ⋅ ec_ij ) (13) where the dimension of the word table of the Embedding layer is
√dk
(dseq, dseq) and hs0 ∈ Rdhs0. Then, the node features and edge features are
input to the initialization block consisting of a LayerNorm and a gvp
l+1
̂ = hl + W l Dropout layer without activation functions, respectively:
hc_i c_i h0
(14)
k, l k, l (hs1 , hv1 ) = gvp (LayerNorm (hs , hv )) (28)
(Concatk∈1, …, H (Aggregation_Sumj∈N(i) (wc_ij vc_ j )))

(es1 , ev1 ) = gvp (LayerNorm (es , ev )) (29)

l+1
̂ = elij + We0
ec_ij l
Dropout (Concatk∈1, …, H (wk, l
c_ij
)) (15)
where hs ∈ Rdseq +dhs0 , hv ∈ Rdhv0 ×3 , hs1 ∈ Rdhs1 , hv1 ∈ Rdhv1 ×3 , es ∈ Rdes0 ,
ev ∈ Rdev0 ×3, es1 ∈ Rdes1 and ev1 ∈ Rdev1 ×3. After initialization, the node and
l+1 l+1
hl+1 ̂ + W l Dropout (SiLU (W l Norm (h ̂ )))
= hc_i (16) edge features are input to the GVPConv layer stacking twice, involving
c_i h2 h1 c_i
gvp layers in message passing. The equations of the GVPConv layer are
as follows:
l+1 ll+1 l l+1
ec_ij ̂ + We2
= ec_ij Dropout (SiLU (We1 ̂ )))
Norm (ec_ij (17)
mls_ij = Concat (hls_i , es_ij
l
, hls_ j ) (30)

where WQk, l , WVk, l , WEk, l ∈ Rdk ×d , and Wh0

WKk, l , l l
, We0 l
∈ Rd×d , and Wh1 ,
k, l
We1 2d×d
∈R l
, and Wh2, We2 l
∈ Rd×2d are learnable parameters from linear mlv_ij = Concat (hlv_i , ev_ij
l
, hlv_ j ) (31)
layers; k ∈ 1, …, H denotes the number of attention heads; dk is the
dimension of each head, which equals d divided by H; j ∈ N(i) represents
(mls_ij_1 , mlv_ij_1 ) = gvp (mls_ij , mlv_ij ) (32)
the neighboring nodes of node i; Norm denotes batch normalization;
Concat denotes the concatenation operation; Dropout denotes the
dropout operation; SiLU represents a type of activation functions; (mls_ij_2 , mlv_ij_2 ) = gvp (mls_ij_1 , mlv_ij_1 ) (33)
Aggregation_Sumj∈N(i) represents aggregating the messages on the edges
connecting node i and its neighboring nodes j by summation; and
(mls_ij_3 , mlv_ij_3 ) = gvp (mls_ij_2 , mlv_ij_2 ) (34)
Softmaxj∈N(i) denotes the SoftMax operation on neighboring nodes j.

Geometric vector perceptrons ̂ l , h ̂ l ) = Aggregation_Mean

(h s_ l l
i∈N( j ) (ms_ij_3 , mv_ij_3 ) (35)
j v_ j
A GVP is implemented in KarmaDock as the protein encoder to update
node embeddings based on topology connections and geometric
features inside and between resides. The basic block of a GVP is the gvp ̂l ) ,
(f s_l̂ j_0 , f v_l̂ j_0 ) = LayerNorm (hls_ j + Dropout (h s_ j
layer that received both scalar features fs ∈ Rd and vector features (36)
̂ l ))
hlv_ j + Dropout (h v_
fv ∈ Rd×3 (Fig. 1d). The forward process of the lth layer is as follows: j

Nature Computational Science | Volume 3 | September 2023 | 789–804 799

Article https://doi.org/10.1038/s43588-023-00511-5

(f s_l̂ j_1 , f v_l̂ j_1 ) = gvp (f s_l̂ j_0 , f v_l̂ j_0 ) (37) where h0, h1 and e1 ∈ Rdh, e0 ∈ Rde, We_init ∈ Rdh ×de and be_init ∈ Rdh are learn-
able parameters in a linear layer.
The basic block used for updating ligand coordinates consists of
(f s_l̂ j_2 , f v_l̂ j_2 ) = gvp (f s_l̂ j_1 , f v_l̂ j_1 ) (38) eight EGNN layers stacked sequentially (Fig. 1f). The message-passing
process of the lth EGNN layer is as follows:
k, l
(hl+1
s_i
, hl+1
v_ j
) = LayerNorm (hls_ j + Dropout (f s_l̂ j_2 ) , (qi )
k∈1, …, H
= WQl hli_1 + blQ (42)
(39)
hv_l j + Dropout (f v_l̂ j_2 ))
k, l
(kj ) = WKl hlj_1 + blK (43)
k∈1, …, H
where equations (32), (33) and (37) implement activation functions of
ReLU and Sigmoid for scalar features and vector features, respectively,
k, l
and other gvp layers using non activation functions; mls_ij ∈ R2dhs1 +des1 , (vj ) = WVl hj_1
l
+ blV (44)
k∈1, …, H
mlv_ij (2dhv1 +dev1 )×3 ,
∈R mls_ij_1 , mls_ij_2 , mls_ij_3 , ̂ l , f l̂
h s_ ̂
, f s_∗l and hl+1 ∈ Rdhs1 ,
j s_ j_ 0 j_ 2 s_i
̂ l , f l̂
mlv_ij_1 , mlv_ij_2 , mlv_ij_3 , h v_ , f v_l̂ j_2 and hl+1 ∈ Rdhv1 ×3 , f s_l̂ j_1 ∈ R4dhs1 ,
j v_ j_0 v_ j eijl = Concat (eij_1
l
, ‖‖xil − xjl ‖‖ ) (45)
2
f v_l̂ j_1 ∈R (2dhv1 )×3 ; and Aggregation_Meani∈N(j) represents averaging
the messages on the edges connecting node j and its neighboring
mlij = Wm2
l l
(LeakyReLU (Dropout (Wm1 elij + blm1 ))) + blm2 (46)
nodes i.

Interaction graph construction k, l

(kij ) = Concatkϵ1, …, H (kjk, l ) ⊙ mlij (47)
To predict the binding poses, we construct the interaction graph kϵ1, …, H

[Gp, c = (Hp, c , Ep, c , Xp, c )]based on the protein graph Gp and ligand graph
Gc, which can consider protein–protein interactions, LL interactions
wijk, l = (qik, l ⊙ kijk, l ) /√dk (48)
and PL interactions. Unlike common methods used in CPI models that
only connect ligand and protein nodes within a certain distance thresh-
old of the ligand atoms, we fully connect protein and ligand nodes
aijk, l = Softmaxj∈N(i) (‖‖wijk, l ‖‖ ) (49)
considering the global PL interactions for accurate binding pose gen- 2
eration due to the unknown PL binding poses. Hence, we add edges
connecting every PL node pair on the basis of the residue graph and ̂ l = Dropout
h i_1
molecular graph. Furthermore, to enable KarmaDock to learn suitable (50)
bond lengths and angles in the molecules, we connect every ligand k, l k, l
(Whl (Concatk∈1, …, H (Aggregation_Sumj∈N(i) (wij ⊙ vj ))) + blh )
node for LL-interaction learning and encode the actual distance
between atoms in every fragment constructed by splitting the ligand
based on rotatable bonds. The node features h0 ∈ Rdh0 of proteins and hl+1 ̂l )
= Gate_Block (hli_1 , h i_1 (51)
i_1
ligands are inherited from the output of the GT encoder and GVP
encoder, respectively. The edge features e0 ∈ Rde0 consist of one-hot
encoding for edge types (single bond, double bond, triple bond, aro-
l+1
eij_1 = Wel Concatk∈1, …, H (αijk, l ) + ble (52)
matic bond and non-bond interaction) and the distance between nodes
(actual distance for edges inside residue graphs and edges between
ligand nodes inside the same fragment, while other edges are encoded ⎛ ⎞
⎜ ⎟
as −1). Furthermore, the node coordinates x0 ∈ Rn×3 consist of protein xil+1 = Coords_Update_Block ⎜(wijk, l ) k ∈ 1, …, H, , xil , (xjl ) (53)
j∈N(i) ⎟
coordinates inherited from the protein graphs and ligand conforma- ⎜ ⎟
⎝ j ∈ N (i) ⎠
tions randomly rotated and translated around the pocket center.
where αk, l
∈ R1; hli_1, hlj_1, eij_1
l ̂ l , hl+1 and el+1 ∈ Rdh; q k, l , k k, l , k k, l ,
, eijl , mlij , h i_1
ij i_1 ij_1 i j ij
E(n) equivariant graph neural network block
EGNN is an E(n) equivariant model capable of handling dynamical vk,
j
l
and wijk, l ∈ Rdk ; WQl , WKl , WVl , Wm2
l
, Whl and Wel ∈ Rdh ×dh; Wm1
l
∈ Rdh ×(dh +1), blQ ,
systems with high speed. It plays the role of an FF, which meets our
blK , blV , blm1 , blm2 , blh and ble ∈ Rdh are learnable parameters from linear
requirement of both E(n) equivariance and fast processing speed. As
transformer architecture is popular for its outstanding performance layers; k ∈ 1, … , H denotes the number of attention heads; dk is the
on various tasks, merging self-attention and graph message passing dimension of each head, which equals dh divided by H; j ∈ N (i) repre-
(for example, RTMScore, LigPose and MedusaGraph) can substantially sents the neighboring nodes of node i; Concat denotes the concatena-
improve the representational ability of GNNs. Similar to LigPose and tion operation; Dropout denotes the dropout operation; LeakyReLU
MedusaGraph, self-attention is also involved in the message-passing is a type of activation function; Aggregation_Sumj∈N(i) represents sum-
process of an EGNN. To increase the accuracy and force for the EGNN ming the messages on the edges connecting node i and its neighboring
layer to predict atom movement based on current binding poses, the nodes j; and Softmaxj∈N(i)denotes the SoftMax operation on neighboring
recycling scheme inspired by AlphaFold2 is utilized, which increases nodes j.
the number of movements. Coords_Update_Block is responsible for updating the coordinates
The scalar node embeddings h0 of proteins and compounds of ligand nodes:
updated by GVP and GT, respectively, are first initialized by graph ⇀

normalization, and the edge features e0 are initialized by a linear layer: Δ xijl = xil − xjl (54)

h1 = GraphNorm (h0 ) (40)

⇀ ⇀
‖ ⇀‖
Δ xijl = Δ xijl /‖Δ xijl ‖ (55)
e1 = We_init e0 + be_init (41) ‖ ‖2

Nature Computational Science | Volume 3 | September 2023 | 789–804 800

Article https://doi.org/10.1038/s43588-023-00511-5

⇀
k, l
Δ xij = Δ xijl ⋅ (Wx2
l l
(LeakeyReLU (Dropout (Wx1 wk, l
+ blx1 ))) + blx2 ) (56)
the MMFF94 FF to optimize the predicted ligand conformations with
ij
a maximum of ten steps. However, because the minimization process
ignores the protein, it may destroy the binding poses predicted by
Δ xijl = WHl Concatk∈1, …, H (Δ xij )
k, l
(57) KarmaDock. Another method aligns the chemically plausible RDkit
conformations, which lack proper orientation and torsional angles,
to the predicted binding poses and replaces the predicted poses with
Δ xil = Aggregation_Sumj∈N(i) (Δ xijl ) (58) the aligned RDkit conformations. The torsional angles of ligands are
first defined and then assigned to the RDkit conformations. Finally, the
transformed RDkit conformations are aligned to the predicted binding
xil+1 = xil + Δ xil (59) conformations by the Kabsch algorithm.
⇀
k, l l 1×3
where xil , xjl , Δ xijl , Δ xij , Δ xi and xil+1 ∈ R ; Wx1l ∈ R(dk /2)×dk , Wx2
l
∈ R1×(dk /2), Dataset
WHl ∈ R1×(H), blx1 ∈ R
(dk /2) 1
and blx2 ∈ R . Most DLSFs and PGMs are trained on the PDBBind dataset26, which con-
sists of high-quality PL complexes and their binding affinities extracted
Gate_Block is a basic block for the residual connection used in from the Protein Data Bank (PDB)37. In this study, the newest PDBBind
EGNN layers and the beginning of each recycling. version 2020 with 19443 PL complexes is used for KarmaDock training
and benchmarking. Additionally, the APObind dataset27, a derivative
̂ , h , ĥ
g = Sigmoid (Dropout (Wg Concat (hnew old new − hold ) + bg )) (60) of the 2019 version of PDBBind, was utilized. Unlike its predecessor,
APObind features apo-protein structures in lieu of holo structures. It
̂ is important to clarify that only the core set of APObind, consisting of
hnew = GraphNorm(g ⊙ hnew + hold ) (61)
229 PL complexes, was used in the testing phase. The CASF 2016 bench-
mark, containing 285 diverse PL complexes, is a gold standard for evalu-
̂ , g and h ϵRdh; W ϵRdh ×dh and b ϵRdh are learnable param-
where hold, hnew ating SFs under four various tasks (scoring power test, docking power
new g g
eters from linear layers. test, ranking power test and screening power test). As KarmaDock is
generally a VS tool, we primarily focus on assessing the docking power
Mixture density network block and screening power of its SF (that is, the MDN block), while ignoring
The MDN block, which has been shown to be effective in binding pose the ranking power and scoring power. To further evaluate the screening
selection and actives enrichment, is used as the scoring module in power of KarmaDock, the DEKOIS 2.0 dataset, consisting of 81 targets
KarmaDock (Fig. 1e). The encoded node embeddings (hp , hc ) of proteins from various protein families with 40 active ligands and 1,200 decoys
and ligands by GVP and GT, respectively, are concated sequentially, per target, is used to simulate a VS test.
followed by a linear layer, a batch normalization layer, an activation Furthermore, the screening libraries of ChemDiv 2022 and Specs
function (exponential linear unit, ELU), and a Dropout layer for PL 2021, with 1,561,007 and 208,780 compounds, respectively, were
interaction capturing. Then, three linear layers are used to determine screened using KarmaDock to discover LTK inhibitors, followed by
a set of means μp, c, standard deviations σp, c and mixing coefficients experiments to further validate the results.
πp, c needed to parametrize a mixture density model encoding a mixture
distribution by n distance distributions for each PL node pair: Dataset preprocessing
All the protein files were downloaded from PDB and preprocessed by
hp, c = Dropout
(62) the Protein Preparation Wizard33 module in Schrödinger 2020, which
(ELU (BatchNorm (Wp, c Concat (hp , hc ) + bp, c ))) involves assigning bond orders and re-adding hydrogens. Next, the pro-
tein structures were repaired by creating necessary bonds to proximal
sulfurs, filling missing side trains and missing loops, and optimizing
μp, c = ELU (Wμ hp, c + bμ ) + 1 (63)
the hydrogen-bond network. Hydrogens were then minimized with
the OPLS3 FF38. PROPKA was used for generating protonation states of
σp, c = ELU (Wσ hp, c + bσ ) + 1.1 (64) residues at a pH of 7.0 and Epik was used to generate the ionized state
of het atoms39,40. After preprocessing, we selected protein residues
within 12 Å of the ligand atoms with the help of Prody as the binding
πp, c = Softmax (Wπ hp, c + bπ ) (65)
pocket, which were used as the input for KarmaDock instead of the
whole proteins. This selection allowed KarmaDock to focus on the
where Wp, c ∈ Rdp, c ×2dh, Wμ , Wσ , Wπ ∈ Rn×dp, c, bp, c ∈ Rdp, c, bμ, bσ and bπ ∈ Rn specific region of the protein that was likely to interact with the ligand
are learnable parameters of linear layers; hp and hc ∈ Rdh; Concat, Soft- and reduces the complexity of the input for the network.
max and Dropout denote the concatenation, softmax and dropout
operations, respectively. Training protocol
As we implement a residue-level coarse-grained representation The training processing was carefully designed. It is reasonable to
of proteins, the minimum distance between a specific ligand atom and assume that the distributions of the PL node pair distances fitted by
each residue atom is selected as the indicator of distance between PL the MDN block can help the model to the search space for binding poses
node pairs inspired by RTMScore. To help the model learn molecular and easily find the best binding conformations. To utilize the distribu-
structures more effectively, two auxiliary tasks are incorporated: pre- tions of the PL node pair distances for docking, we first trained Karma-
dicting atom type and bond type inside protein and ligand nodes based Dock as an SF (that is, the MDN block), using the node embeddings
on the previously learned ligand node representation (hp , hc ). updated by encoders and the ground-truth binding conformations as
inputs, with an MDN loss function LMDN and two cross-entropy loss
Post-processing functions (Latom , Lbond ) for two auxiliary tasks, respectively:
To ensure the validity of bond lengths and angles, FF optimization and
L = LMDN + 0.001 × Latom + 0.001 × Lbond (66)
RDkit-conformation alignment are studied in this Article. FF optimi-
zation can be easily implemented by an Application Programming
Interface (API) of RDkit named MMFFOptimizeMolecule, which uses LMDN = −logP ((dp, c , |, hp , hc ))

Nature Computational Science | Volume 3 | September 2023 | 789–804 801

Article
10
= −log ∑ πp, c, n N ((dp, c , |, μp, c, n , σp, c, n ))
n=1
where μp, c, n, σp, c, n and πp, c, n represent the mean, s.d. and mixing coef-
ficients of the nth distance distribution; hp, hc and dp, c represent the
node embeddings of protein nodes, ligand nodes and the distance
between PL nodes, respectively. The model was optimized using the
Adam optimizer with a batch size of 64, a learning rate of 1 × 10−3 and a
weight decay of 1 × 10−5. The training was stopped if the loss on the
validation set continuously increased for 70 epochs. After that, the GT
encoder and GVP encoder are believed to have partially learned the
distance distributions. We then trained the docking module as well as
the trained scoring module using the same dataset split method as
used in the scoring module training process. The loss function of the
docking module was added to equation (68) with a weight of 1 based
on the calculated r.m.s.d. between predicted ligand conformations
and the ground-truth conformations. The training hyperparameters
were the same as before except that the learning rate was set to 1 × 10−4
and the weight decay was canceled:
L = Ldocking + LMDN + 0.001 × Latom + 0.001 × Lbond
√ N
√ pred
2 simplified molecular-input line-entry system (SMILES) and their IC50
√ ∑n=1 (xl, n − xlabel
l, n
) values are documented comprehensively in Supplementary Table 4.
pred
Ldocking = r.m.s.d. (xl , xllabel ) = (69)
√ N
where N denotes the number of ligand nodes and n the index of the
ligand nodes.
Evaluation protocol
KarmaDock is a versatile tool that can be used as an SF, a PGM and a
ligand-docking tool. When used as an SF with given binding poses, Kar-
maDock can calculate MDN scores based on the protein and the ligand
node embeddings from encoders, and the binding conformations.
When used as a PGM, the ligand conformation should be first gener-
ated by RDkit and then initialized by random rotating and translating
around the pocket center. The encoded node embeddings along with
pocket conformations and ligand conformations are then input to
the EGNN block to generate binding poses. If used as a ligand-docking
tool, KarmaDock first predicts the binding poses and then scores the
binding poses using the MDN block.
Metrics
Unlike DLSFs or PGMs, it is crucial for a docking tool to consider not only
one, but multiple criteria, including docking speed, binding pose qual-
ity, and binding strength prediction accuracy. In this study we assessed
KarmaDock by examining its performance as a PGM in terms of its dock-
ing speed and accuracy. The docking speed was simply measured by the
time it took to generate a single binding pose, while the docking accuracy
was measured by the success rate of generating binding conformations
with an r.m.s.d. of less than 2 Å from the ground-truth conformations.
Furthermore, the performance of KarmaDock as an SF was also evaluated.
In evaluating the performance of SFs, we prioritized the screening power
and docking power over scoring power. Here, the docking power was cal-
culated as the success rate and the screening power was mainly measured
by BEDROC (α = 80.5) (ref. 34) and enrichment factor calculated from
the top x% samples (EF_x%, x = 0.5, 1, 5). Also, two metrics evaluating
the ranking ability of DL models, the area under the receiver operating
characteristic curve (ROC_AUC)34 and the area under the precision-recall
curve (PRAUC), are also included in this study as axillary metrics in VS.
VS workflow targeting LTK
As no experimentally determined 3D structure is available in the PDB,
SWISS-MODEL36 was used for protein homology modeling and protein
Nature Computational Science | Volume 3 | September 2023 | 789–804
https://doi.org/10.1038/s43588-023-00511-5
structure generation, where the ALK structure (PDB 4CLI) with high
(67) sequence similarity to LTK was utilized as the template structure. The
protein structure was prepared by the Protein Preparation Wizard33
module in Schrödinger 2020. The compounds from the ChemDiv and
Specs databases were collected for screening. Then, KarmaDock was
used for screening the compound library. The top 1,000 scored mol-
ecules were selected and subjected to drug-likeness filtering based
on Lipinski’s rule of five. This rule, widely accepted in pharmaceutical
research, helps evaluate which compounds have properties compatible
with good absorption and permeability in the human body. As a result,
we were left with a refined set of molecules with greater potential to be
active and drug-like inhibitors. Subsequently, the selected molecules
underwent clustering based on their extended connectivity finger-
prints. The outcome of this step was 25 distinct clusters of structurally
and chemically related molecules. We visually analyzed each group
in terms of interaction modes between protein and ligands. From
each cluster, we identified and selected the molecule with the most
favorable interaction pattern, resulting in 25 top-tier candidates for
further evaluation. These chosen molecules were then purchased for
biological activity testing using the MTT assay. Upon setting a threshold
of 5 μM for the IC50, an approximate hit rate of 24.0% (6 out of 25) was
(68)
discerned. Subsequently, adopting a criterion of 10 μM for IC50, the hit
rate was found to be 72.0% (18 out of 25). The specific compound IDs,
MTT procedure
This study used the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetra-
zolium bromide) assay to gauge compound activity in the engineered
Ba/F3-CLIP1-LTK cell line that grows only on LTK activity. The experi-
ment began by preparing a cell suspension of the Ba/F3-CLIP1-LTK
cells using RPMI-1640 medium, a nutrient-rich medium commonly
used in cell culture that is devoid of interleukin-3. This suspension was
aliquoted into a 96-well plate, with each well receiving 90 μl, equating to
~105 cells. Post 4 h of undisturbed incubation in a controlled cell-culture
environment, the test compounds (whose concentrations were varied
in a gradient across wells) or the control compound (dimethylsulfoxide,
DMSO) were added in a volume of 10 μl. The cells were then allowed
to grow for 72 h, then MTT reagent (at a concentration of 5 mg ml−1)
was subsequently added to each well and incubated for 4 h. The MTT
was reduced by metabolically active cells to form insoluble formazan
crystals. To solubilize these crystals, 100 μl of SDS-HCl-PBS tri-buffer
solution was added and the plate was left overnight. Absorbance values
at 570 nm, representing the amount of solubilized formazan and thus
the cell metabolic activity, were recorded using a microplate reader.
By fitting a dose–response curve, the IC50 value for the test compound
could be obtained, providing a quantitative measure of the compound’s
ability to inhibit CLIP1-LTK activity in cells.
Other protocol
KarmaDock was trained using eight NVIDIA A100-SXM4-80GB GPUs
and 64 core Intel(R) Xeon(R) platinum 8358P CPUs @ 2.60 GHz. All
the traditional docking tools were evaluated using 48 core Intel(R)
Xeon(R) Gold 6240R CPUs @ 2.40 GHz, and the DL models were tested
on a single Tesla V100S-PCIE-32GB GPU. The r.m.s.d. values between
generated binding poses and crystallized binding poses were cal-
culated by the obrms module of OpenBabel. Recognition of eight
common non-bond interactions, including acceptor–metal, π–metal,
π–cation, π–stacking, salt bridges, halogen bonds, hydrogen bonds and
hydrophobic contacts, was implemented through the APIs provided
by oddt41. For traditional ligand docking, the origination of the initial
ligand conformations was executed with RDkit, as opposed to leverag-
ing the crystal conformation. For the AutoDock GPU, the grid size was
(60 Å, 60 Å, 60 Å). All other docking parameters were maintained at
their default settings.
802
Article
Statistics and reproducibility
We trained and evaluated KarmaDock following the convention of
molecular docking studies, where three widely used dataset split
strategies were used and four classic benchmarks were involved in
the assessment. The sample size was near to the sample size in the
benchmarks, and some samples (compounds) were dropped as RDkit
failed to process them. During the training process, the training set
and validation set were randomly selected with a random seed of 42.
The README file in the GitHub repository provided comprehensive
instructions for reproduction.
Reporting summary
Further information on research design is available in the Nature Port-
folio Reporting Summary linked to this Article.
Data availability
The raw datasets26–29 are available at http://pdbbind.org.cn/index.php,
https://github.com/devalab/Apobind and http://www.pharmchem.
uni-tuebingen.de/dekois/data/DEKOIS2.0_library/DEKOIS2.0_library.
rar. The prepared datasets42–44 are available at https://zenodo.org/
record/7788083, https://zenodo.org/record/8211452 and https://
zenodo.org/record/8131256. PDB IDs 1S38, 1SQA, 4JXS, 1PS3, 3DXG,
3D4Z, 4CLI, 4JSZ and 4CTB are available in the Protein Data Bank
(https://www.rcsb.org/)37. Source data are available with this paper.
Code availability
The source code is available at Zenodo (https://zenodo.org/
record/8211513)45 and GitHub (https://github.com/schrojunzhang/
KarmaDock).
References
1. Shen, C. et al. From machine learning to deep learning: advances
in scoring functions for protein-ligand docking. WIREs Comput.
Mol. Sci. 10, e1429 (2020).
2. Morris, G. M. et al. AutoDock4 and AutoDockTools4: automated
docking with selective receptor flexibility. J. Comput. Chem. 30,
2785–2791 (2009).
3. Eberhardt, J., Santos-Martins, D., Tillack, A. F. & Forli, S.
AutoDock Vina 1.2.0: new docking methods, expanded force field
and Python bindings. J. Chem. Inf. Model. 61, 3891–3898
(2021).
4. Zhao, H. & Caflisch, A. Discovery of ZAP70 inhibitors by high-
throughput docking into a conformation of its kinase domain
generated by molecular dynamics. Bioorg. Med. Chem. Lett. 23,
5721–5726 (2013).
5. Friesner, R. A. et al. Glide: a new approach for rapid, accurate
docking and scoring. 1. Method and assessment of docking
accuracy. J. Med. Chem. 47, 1739–1749 (2004).
6. Jones, G., Willett, P., Glen, R. C., Leach, A. R. & Taylor, R.
Development and validation of a genetic algorithm for flexible
docking. J. Mol. Biol. 267, 727–748 (1997).
7. Irwin, J. J. et al. ZINC20—a free ultralarge-scale chemical
database for ligand discovery. J. Chem. Inf. Model. 60, 6065–6073
(2020).
8. Alhossary, A., Handoko, S. D., Mu, Y. & Kwoh, C.-K. Fast, accurate
and reliable molecular docking with QuickVina 2. Bioinformatics
31, 2214–2216 (2015).
9. Santos-Martins, D. et al. Accelerating AutoDock4 with GPUs
and gradient-based local search. J. Chem. Theory Comput. 17,
1060–1073 (2021).
10. Jumper, J. et al. Highly accurate protein structure prediction with
AlphaFold. Nature 596, 583–589 (2021).
11. Zhang, H. et al. SDEGen: learning to evolve molecular
conformations from thermodynamic noise for conformation
generation. Chem. Sci 14, 1557–1568 (2023).
Nature Computational Science | Volume 3 | September 2023 | 789–804
https://doi.org/10.1038/s43588-023-00511-5
12. Jing, B., Corso, G., Chang, J., Barzilay, R. & Jaakkola, T. Torsional
diffusion for molecular conformer generation. in Advances in
Neural Information Processing Systems (eds. Koyejo, S. et al.) Vol.
35, 24240–24253 (Curran Associates, Inc., 2022).
13. Xu, M. et al. GeoDiff: a geometric diffusion model for molecular
conformation generation. in International Conference on Learning
Representations (2022).
14. Zhang, Y., Cai, H., Shi, C. & Tang, J. E3Bind: an end-to-end
equivariant network for protein-ligand docking. in International
Conference on Learning Representations (2023).
15. Stärk, H., Ganea, O., Pattanaik, L., Barzilay, D. R. & Jaakkola, T.
EquiBind: geometric deep learning for drug binding structure
prediction. in Proceedings of the 39th International Conference on
Machine Learning 20503–20521 (PMLR, 2022).
16. Qiao, Z., Nie, W., Vahdat, A., Miller III, T. F. & Anandkumar, A.
State-specific protein-ligand complex structure prediction with
a multi-scale deep generative model. Preprint at arXiv https://doi.
org/10.48550/arXiv.2209.15171 (2023).
17. Lu, W. et al. TANKBind: trigonometry-aware neural networKs for
drug-protein binding structure prediction. in Advances in
Neural Information Processing Systems Vol. 35, 7236–7249
(2022).
18. Junfeng, Z., Kelei, H., Tiejun, D. & Wu, J. Accurate protein-ligand
complex structure prediction using geometric deep learning. Res.
Square https://doi.org/10.21203/rs.3.rs-1454132/v1 (2022).
19. Corso, G., Stärk, H., Jing, B., Barzilay, R. & Jaakkola, T. S. DiffDock:
diffusion steps, twists, and turns for molecular docking.
Preprint at arXiv https://doi.org/10.48550/arXiv.2210.01776
(2023).
20. Satorras, V. G., Hoogeboom, E. & Welling, M. E(n) equivariant
graph neural networks. in Proceedings of the 38th International
Conference on Machine Learning (eds. Meila, M. & Zhang, T.) Vol.
139, 9323–9332 (PMLR, 2021).
21. Ho, J., Jain, A. & Abbeel, P. Denoising diffusion probabilistic
models. In Advances in Neural Information Processing Systems
(eds Larochelle, H. et al.) Vol. 33, 6840–6851 (Curran Associates,
2020).
22. Hu, X. et al. Discovery of novel non-steroidal selective
glucocorticoid receptor modulators by structure- and IGN-
based virtual screening, structural optimization and biological
evaluation. Eur. J. Med. Chem. 237, 114382 (2022).
23. Hu, X. et al. Discovery of novel GR ligands toward druggable
GR antagonist conformations identified by MD simulations and
Markov state model analysis. Adv. Sci. 9, 2102435 (2022).
24. Shen, C. et al. Boosting protein-ligand binding pose prediction
and virtual screening based on residue-atom distance likelihood
potential and graph transformer. J. Med. Chem. 65, 10691–10706
(2022).
25. Jing, B., Eismann, S., Suriana, P., Townshend, R. J. L. & Dror,
R. Learning from protein structure with geometric vector
perceptrons. in International Conference on Learning
Representations (2021).
26. Liu, Z. et al. Forging the basis for developing protein-ligand
interaction scoring functions. Acc. Chem. Res. 50, 302–309
(2017).
27. Aggarwal, R., Gupta, A. & Priyakumar, U. D. APObind: a dataset
of ligand unbound protein conformations for machine learning
applications in de novo drug design. Preprint at arXiv https://doi.
org/10.48550/arXiv.2108.09926 (2021).
28. Su, M. et al. Comparative assessment of scoring functions: the
CASF-2016 update. J. Chem. Inf. Model. 59, 895–913 (2019).
29. Bauer, M. R., Ibrahim, T. M., Vogel, S. M. & Boeckler, F. M.
Evaluation and optimization of virtual screening workflows with
DEKOIS 2.0—a public library of challenging docking benchmark
sets. J. Chem. Inf. Model. 53, 1447–1462 (2013).
803
Article
30. Friesner, R. A. et al. Extra precision glide: docking and
scoring incorporating a model of hydrophobic enclosure
for protein-ligand complexes. J. Med. Chem. 49, 6177–6196
(2006).
31. Wang, Z. et al. Comprehensive evaluation of ten docking
programs on a diverse set of protein-ligand complexes: the
prediction accuracy of sampling power and scoring power. Phys.
Chem. Chem. Phys. 18, 12964–12975 (2016).
32. Jain, A. N. Surflex-Dock 2.1: robust performance from ligand
energetic modeling, ring flexibility and knowledge-based search.
J. Comput. Aided Mol. Des. 21, 281–306 (2007).
33. Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R.
& Sherman, W. Protein and ligand preparation: parameters,
protocols and influence on virtual screening enrichments.
J. Comput. Aided Mol. Des. 27, 221–234 (2013).
34. Truchon, J.-F. & Bayly, C. I. Evaluating virtual screening methods:
good and bad metrics for the ‘early recognition’ problem.
J. Chem. Inf. Model. 47, 488–508 (2007).
35. Izumi, H. et al. The CLIP1-LTK fusion is an oncogenic driver in non-
small-cell lung cancer. Nature 600, 319–323 (2021).
36. Waterhouse, A. et al. SWISS-MODEL: homology modelling of
protein structures and complexes. Nucleic Acids Res. 46, W296–
W303 (2018).
37. Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28,
235–242 (2000).
38. Kaminski, G. A., Friesner, R. A., Tirado-Rives, J. & Jorgensen, W.
L. Evaluation and reparametrization of the OPLS-AA force field
for proteins via comparison with accurate quantum chemical
calculations on peptides. J. Phys. Chem. B 105, 6474–6487
(2001).
39. Olsson, M. H. M., Søndergaard, C. R., Rostkowski, M. & Jensen,
J. H. PROPKA3: consistent treatment of internal and surface
residues in empirical pKa predictions. J. Chem. Theory Comput. 7,
525–537 (2011).
40. Shelley, J. C. et al. Epik: a software program for pK(a) prediction
and protonation state generation for drug-like molecules. J.
Comput. Aided Mol. Des. 21, 681–691 (2007).
41. Wójcikowski, M., Zielenkiewicz, P. & Siedlecki, P. Open Drug
Discovery Toolkit (ODDT): a new open-source player in the drug
discovery field. J. Cheminform. 7, 26 (2015).
42. Zhang, X. J. APObind core set for KarmaDock (229 protein-ligand
complexes) Zenodo https://doi.org/10.5281/zenodo.8211452
(2023).
43. Zhang, X. J. DEKOIS2.0 for KarmaDock Zenodo https://doi.
org/10.5281/zenodo.8131256 (2023).
44. Zhang, X. J. KarmaDock_PDBBind2020_coreset (1.0) Zenodo
https://doi.org/10.5281/zenodo.7788083 (2023).
45. Zhang, X. J. schrojunzhang/KarmaDock: v1.0.0 Zenodo https://doi.
org/10.5281/zenodo.8211513 (2023).
Nature Computational Science | Volume 3 | September 2023 | 789–804
https://doi.org/10.1038/s43588-023-00511-5
Acknowledgements
This work was financially supported by the National Key Research
and Development Program of China (2022YFF1203000), the National
Natural Science Foundation of China (22220102001, 82204279 and
22007082), the Natural Science Foundation of Zhejiang Province
(LD22H300001 and LQ21B030013) and Fundamental Research Funds
for the Central Universities (226-2022-00220). We also thank L. Xu
at Jiangsu University of Technology for preparing all the compounds
used in this study based on the Glide module in Schrödinger software,
which substantially contributed to our research.
Author contributions
X.Z., O.Z. and C.S. developed this method, analyzed the data and
wrote the manuscript. W.Q. and S.C. bought the compounds and
measured their IC50 values. H.C., Y.K., Z.W., E.W., J.Z., Y.D., F.L., T.W.,
H.D. and L.W. evaluated and interpreted the results and wrote the
manuscript. P.P., G.C., C.-Y.H. and T.H. conceived and supervised the
project, interpreted the results and wrote the manuscript. All authors
read and approved the final manuscript.
Competing interests
The authors declare no competing interests.
Additional information
Supplementary information The online version contains supplementary
material available at https://doi.org/10.1038/s43588-023-00511-5.
Correspondence and requests for materials should be addressed to
Peichen Pan, Guangyong Chen, Chang-Yu Hsieh or Tingjun Hou.
Peer review information Nature Computational Science thanks
Matthew Holcomb and Shina Kamerlin for their contribution to the
peer review of this work. Primary Handling Editor: Kaitlin McCardle, in
collaboration with the Nature Computational Science team.
Reprints and permissions information is available at
www.nature.com/reprints.
Publisher’s note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations.
Springer Nature or its licensor (e.g. a society or other partner) holds
exclusive rights to this article under a publishing agreement with
the author(s) or other rightsholder(s); author self-archiving of the
accepted manuscript version of this article is solely governed by the
terms of such publishing agreement and applicable law.
© The Author(s), under exclusive licence to Springer Nature America,
Inc. 2023
804