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Development and evaluation of a deep learning model for protein-ligand binding affinity prediction
19 December 2017
Marta M. Stepniewska-Dziubinska
P. Zielenkiewicz
P. Siedlecki
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Papers citing
"Development and evaluation of a deep learning model for protein-ligand binding affinity prediction"
37 / 37 papers shown
A Geometric Graph-Based Deep Learning Model for Drug-Target Affinity Prediction
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Hybrid Quantum Neural Networks for Efficient Protein-Ligand Binding Affinity Prediction
Seon-Geun Jeong
Kyeong-Hwan Moon
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120
1
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14 Sep 2025
KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction
Han Liu
Keyan Ding
Peilin Chen
Yinwei Wei
Liqiang Nie
Dapeng Oliver Wu
Shiqi Wang
197
0
0
16 Jun 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery
Yiheng Zhu
Mingyang Li
Junlong Liu
Kun Fu
Jian Wu
Yue Liu
Mingze Yin
Jieping Ye
Jian Wu
Xiping Hu
334
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0
06 Mar 2025
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information
bioRxiv (bioRxiv), 2023
Taojie Kuang
Yiming Ren
Zhixiang Ren
363
15
0
28 Sep 2023
A hybrid quantum-classical fusion neural network to improve protein-ligand binding affinity predictions for drug discovery
International Conference on Quantum Computing and Engineering (QCE), 2023
L. Domingo
M. Chehimi
S. Banerjee
S. H. Yuxun
S. Konakanchi
L. Ogunfowora
S. Roy
S. Selvaras
M. Djukic
C. Johnson
AI4CE
196
13
0
06 Sep 2023
Machine Learning Small Molecule Properties in Drug Discovery
Artificial Intelligence Chemistry (AIC), 2023
Nikolai Schapin
Maciej Majewski
Alejandro Varela-Rial
C. Arroniz
Gianni De Fabritiis
160
29
0
02 Aug 2023
Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach
ACM International Conference on Computing Frontiers (CF), 2023
G. Palermo
Gianmarco Accordi
Davide Gadioli
Emanuele Vitali
Cristina Silvano
...
Eric Lindahl
D. Gregori
Emanuele Sana
Silvano Coletti
P. Gschwandtner
ELM
158
6
0
19 Apr 2023
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations
Derek Jones
Jonathan E. Allen
Xiaohua Zhang
Behnam Khaleghi
Jaeyoung Kang
Weihong Xu
Niema Moshiri
Tajana Rosing
108
4
0
27 Mar 2023
Geometric Graph Learning with Extended Atom-Types Features for Protein-Ligand Binding Affinity Prediction
M. Rana
D. Nguyen
72
18
0
15 Jan 2023
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction
Journal of Chemical Information and Modeling (JCIM), 2022
Gregory W. Kyro
Rafael I. Brent
Victor S. Batista
218
52
0
23 Dec 2022
Dynamic Molecular Graph-based Implementation for Biophysical Properties Prediction
C. Knutson
G. Panapitiya
R. Varikoti
Neeraj Kumar
AI4CE
189
1
0
20 Dec 2022
Recent Developments in Structure-Based Virtual Screening Approaches
C. Gorgulla
90
0
0
06 Nov 2022
Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network
Yi Yi
Xu Wan
Kangfei Zhao
Ou-Yang Le
Pei-Ying Zhao
155
1
0
27 Oct 2022
Predicting Protein-Ligand Binding Affinity via Joint Global-Local Interaction Modeling
Industrial Conference on Data Mining (IDM), 2022
Yang Zhang
G. Zhou
Zhewei Wei
Hongteng Xu
152
12
0
18 Sep 2022
Graph Neural Networks for Molecules
Yuyang Wang
Zijie Li
A. Farimani
GNN
AI4CE
349
51
0
12 Sep 2022
Bridging the gap between target-based and cell-based drug discovery with a graph generative multi-task model
Journal of Chemical Information and Modeling (JCIM), 2022
F. Hu
Dongqi Wang
Huazhen Huang
Yishen Hu
P. Yin
93
3
0
09 Aug 2022
SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction
ACS Omega (ACS Omega), 2022
Shuke Zhang
Yan Jin
Tianmeng Liu
Qi Wang
Zhaohui Zhang
Shuliang Zhao
Bo Shan
209
47
0
25 May 2022
Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinity
Information Sciences (Inf. Sci.), 2022
Zhaoyang Chu
Shichao Liu
Wen Zhang
148
57
0
22 Mar 2022
Learning to Discover Medicines
International Journal of Data Science and Analysis (JDSA), 2022
T. Nguyen
Thin Nguyen
T. Tran
173
2
0
14 Feb 2022
Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks
C. Knutson
Mridula Bontha
Jenna A. Bilbrey
Neeraj Kumar
140
38
0
30 Nov 2021
APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Design
Rishal Aggarwal
Akash Gupta
U. Priyakumar
117
13
0
23 Aug 2021
Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity
Knowledge Discovery and Data Mining (KDD), 2021
Shuangli Li
Jingbo Zhou
Tong Xu
Liang Huang
Fan Wang
Haoyi Xiong
Weili Huang
Dejing Dou
Hui Xiong
MLAU
266
199
0
21 Jul 2021
A Novel Framework Integrating AI Model and Enzymological Experiments Promotes Identification of SARS-CoV-2 3CL Protease Inhibitors and Activity-based Probe
F. Hu
Lei Wang
Yishen Hu
Dongqi Wang
Weijie Wang
Jiaqiang Jiang
Nan Li
P. Yin
98
12
0
29 May 2021
Distance-aware Molecule Graph Attention Network for Drug-Target Binding Affinity Prediction
Jingbo Zhou
Shuangli Li
Liang Huang
Haoyi Xiong
Fan Wang
Tong Xu
Hui Xiong
Dejing Dou
GNN
121
14
0
17 Dec 2020
Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models
Tomohide Masuda
Matthew Ragoza
D. Koes
DiffM
265
58
0
16 Oct 2020
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction
IEEE/ACM Transactions on Computational Biology & Bioinformatics (TCBB), 2020
T. Nguyen
Thin Nguyen
T. Le
T. Tran
GNN
211
72
0
25 Sep 2020
PIGNet: A physics-informed deep learning model toward generalized drug-target interaction predictions
Seokhyun Moon
Wonho Zhung
Soojung Yang
Jaechang Lim
W. Kim
232
129
0
22 Aug 2020
A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19
Jianguo Chen
KenLi Li
Zhaolei Zhang
Keqin Li
Philip S. Yu
248
111
0
04 Jul 2020
Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference
Derek Jones
Hyojin Kim
Xiaohua Zhang
A. Zemla
Garrett A. Stevenson
W. D. Bennett
D. Kirshner
Sergio E. Wong
F. Lightstone
Jonathan E. Allen
AI4CE
123
211
0
17 May 2020
Autonomous discovery in the chemical sciences part I: Progress
Connor W. Coley
Natalie S. Eyke
K. Jensen
182
244
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30 Mar 2020
DeepSurf: A surface-based deep learning approach for the prediction of ligand binding sites on proteins
Stelios K. Mylonas
A. Axenopoulos
P. Daras
159
101
0
13 Feb 2020
Persistent spectral based machine learning (PerSpect ML) for drug design
Zhenyu Meng
Kelin Xia
69
14
0
03 Feb 2020
Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition
S. Raschka
Benjamin Kaufman
AI4CE
313
84
0
17 Jan 2020
DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2019
Yanjun Li
M. Rezaei
Chenglong Li
Xiaolin Li
D. Wu
3DV
197
77
0
01 Dec 2019
Improving detection of protein-ligand binding sites with 3D segmentation
Marta M. Stepniewska-Dziubinska
P. Zielenkiewicz
P. Siedlecki
MedIm
110
99
0
13 Apr 2019
WideDTA: prediction of drug-target binding affinity
Hakime Öztürk
E. Olmez
Arzucan Özgür
OOD
177
189
0
04 Feb 2019
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