Papers citing 'Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity'

Title
A Modular Open Source Framework for Genomic Variant Calling Ankita Vaishnobi Bisoi Shreyas V Jose Siguenza Bharath Ramsundar BDL 189 1 0 18 Nov 2024
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities Charlotte Bunne Yusuf Roohani Yanay Rosen Ankit Gupta Xikun Zhang ... Theofanis Karaletsos Aviv Regev Emma Lundberg J. Leskovec Stephen R. Quake 263 71 0 18 Sep 2024
Open Source Infrastructure for Automatic Cell Segmentation Aaron Rock Menezes Bharath Ramsundar SSeg VLM 181 0 0 12 Sep 2024
Enhancing Neural Subset Selection: Integrating Background Information into Set RepresentationsInternational Conference on Learning Representations (ICLR), 2024 Binghui Xie Yatao Bian Kaiwen Zhou Yongqiang Chen Peilin Zhao Bo Han Wei Meng James Cheng 146 1 0 05 Feb 2024
Open-Source Fermionic Neural Networks with Ionic Charge Initialization Shai Pranesh Shang Zhu Venkat Viswanathan Bharath Ramsundar 116 0 0 16 Jan 2024
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems Shuo-feng Zhang Yang Liu Lei Xie AI4CE GNN PINN 210 18 0 19 Nov 2023
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation Ali Khodabandeh Yalabadi Mehdi Yazdani-Jahromi Niloofar Yousefi Aida Tayebi Sina Abdidizaji O. Garibay 68 4 0 04 Nov 2023
Improved prediction of ligand-protein binding affinities by meta-modelingJournal of Chemical Information and Modeling (JCIM), 2023 Ho-Joon Lee Prashant S. Emani Mark B. Gerstein 139 5 0 05 Oct 2023
Open Source Infrastructure for Differentiable Density Functional Theory Advika Vidhyadhiraja Arun Pa Thiagarajan Shang Zhu Venkat Viswanathan Bharath Ramsundar 90 0 0 27 Sep 2023
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity PredictionJournal of Chemical Information and Modeling (JCIM), 2022 Gregory W. Kyro Rafael I. Brent Victor S. Batista 188 49 0 23 Dec 2022
Recent Developments in Structure-Based Virtual Screening Approaches C. Gorgulla 84 0 0 06 Nov 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 299 48 0 12 Sep 2022
Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes Shuo-feng Zhang Yang Liu Lei Xie GNN AI4CE 139 13 0 06 Jun 2022
Learning Neural Set Functions Under the Optimal Subset OracleNeural Information Processing Systems (NeurIPS), 2022 Chinmay Pani Qifeng Bai Qinliang Su Yingzhen Li P. Zhao Yatao Bian BDL 273 10 0 03 Mar 2022
Learning to Discover MedicinesInternational Journal of Data Science and Analysis (JDSA), 2022 T. Nguyen Thin Nguyen T. Tran 158 2 0 14 Feb 2022
A critical look at the current train/test split in machine learning Jimin Tan Jianan Yang Sai Wu Gang Chen Jake Zhao OOD 116 54 0 08 Jun 2021
High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion ModelsInternational Conference for High Performance Computing, Networking, Storage and Analysis (SC), 2021 Garrett A. Stevenson Derek Jones Hyojin Kim W. D. Bennett B. Bennion ... A. Zemla Xiaohua Zhang Fangqiang Zhu F. Lightstone Jonathan E. Allen 162 17 0 09 Apr 2021
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance ComputersInterface Focus (IF), 2021 Agastya P. Bhati S. Wan Dario Alfè Austin R. Clyde Mathis Bode ... A. Partin Fangfang Xia Xiaotan Duan Rick L. Stevens P. V. Coveney 155 28 0 04 Mar 2021
Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures Shuo-feng Zhang Yang Liu Lei Xie GNN 144 66 0 15 Nov 2020
Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact PredictionbioRxiv (bioRxiv), 2020 Yuning You Yang Shen 164 8 0 14 Nov 2020
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM MedIm 262 35 0 17 Oct 2020
GEFA: Early Fusion Approach in Drug-Target Affinity PredictionIEEE/ACM Transactions on Computational Biology & Bioinformatics (TCBB), 2020 T. Nguyen Thin Nguyen T. Le T. Tran GNN 176 69 0 25 Sep 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 82 207 0 17 May 2020
Multi-View Self-Attention for Interpretable Drug-Target Interaction PredictionJournal of Biomedical Informatics (JBI), 2020 Brighter Agyemang Wei-Ping Wu Michael Y. Kpiebaareh Zhihua Lei Ebenezer Nanor Lei Chen 116 31 0 01 May 2020
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and ContactsbioRxiv (bioRxiv), 2019 Mostafa Karimi Di Wu Zinan Lin Yang Shen 207 51 0 29 Dec 2019
Energy-based Graph Convolutional Networks for Scoring Protein Docking ModelsbioRxiv (bioRxiv), 2019 Yue Cao Yang Shen 95 49 0 28 Dec 2019
TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular NetworkJournal of Chemical Information and Modeling (JCIM), 2019 Yanxing Wang Jianxing Hu Junyong Lai Yibo Li Hongwei Jin L. Zhang L. Zhang Zhenming Liu MedIm 231 13 0 24 Dec 2019
libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning ApplicationsJournal of Chemical Information and Modeling (JCIM), 2019 Jocelyn Sunseri D. Koes AI4CE 118 37 0 10 Dec 2019
Drug-Target Indication Prediction by Integrating End-to-End Learning and Fingerprints Brighter Agyemang Wei-Ping Wu Michael Y. Kpiebaareh Ebenezer Nanor 126 3 0 03 Dec 2019
DeepAtom: A Framework for Protein-Ligand Binding Affinity PredictionIEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2019 Yanjun Li M. Rezaei Chenglong Li Xiaolin Li D. Wu 3DV 169 76 0 01 Dec 2019
Predicting drug-target interaction using 3D structure-embedded graph representations from graph neural networks Jaechang Lim Seongok Ryu Kyubyong Park Yo Joong Choe Jiyeon Ham W. Kim GNN 55 5 0 17 Apr 2019
Uncertainty quantification of molecular property prediction with Bayesian neural networks Seongok Ryu Yongchan Kwon W. Kim BDL 128 20 0 20 Mar 2019
WideDTA: prediction of drug-target binding affinity Hakime Öztürk E. Olmez Arzucan Özgür OOD 169 187 0 04 Feb 2019
Drug cell line interaction prediction Pengfei Liu 117 125 0 28 Dec 2018
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Daniil Polykovskiy Alexander Zhebrak Benjamín Sánchez-Lengeling Sergey Golovanov Oktai Tatanov ... Simon Johansson Hongming Chen Sergey I. Nikolenko Alán Aspuru-Guzik Alex Zhavoronkov ELM 544 751 0 29 Nov 2018
Uncertainty quantification of molecular property prediction using Bayesian neural network models Seongok Ryu Yongchan Kwon W. Kim BDL 114 2 0 19 Nov 2018
Capsule Networks for Protein Structure Classification and Prediction D. R. D. Jesus Julian Cuevas Wilson Rivera S. Crivelli GNN 124 16 0 22 Aug 2018
PADME: A Deep Learning-based Framework for Drug-Target Interaction Prediction Qingyuan Feng Evgenia V. Dueva Artem Cherkasov Martin Ester 202 96 0 25 Jul 2018
End-to-End Learning on 3D Protein Structure for Interface PredictionNeural Information Processing Systems (NeurIPS), 2018 Raphael J. L. Townshend Rishi Bedi Patricia Suriana R. Dror 3DV 303 109 0 03 Jul 2018
DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks Mostafa Karimi Di Wu Zinan Lin Yang Shen 132 387 0 20 Jun 2018
ToxicBlend: Virtual Screening of Toxic Compounds with Ensemble Predictors M. Zaslavskiy S. Jégou Eric W. Tramel G. Wainrib 100 25 0 12 Jun 2018
PotentialNet for Molecular Property PredictionACS Central Science (ACS Cent. Sci.), 2018 Evan N. Feinberg Debnil Sur Zhenqin Wu B. Husic Huanghao Mai Yang Li Saisai Sun Jianyi Yang Bharath Ramsundar Vijay S. Pande 175 387 0 12 Mar 2018
Visualizing Convolutional Neural Network Protein-Ligand Scoring Joshua E. Hochuli Alec Helbling Tamar Skaist Matthew Ragoza D. Koes FAtt 99 68 0 06 Mar 2018
Edge Attention-based Multi-Relational Graph Convolutional Networks Chao Shang Qinqing Liu Ko-Shin Chen Jiangwen Sun Jin Lu Jinfeng Yi J. Bi GNN 232 95 0 14 Feb 2018
DeepDTA: Deep Drug-Target Binding Affinity Prediction Hakime Öztürk E. Olmez Arzucan Özgür 435 1,233 0 30 Jan 2018
Adaptive Graph Convolutional Neural Networks Ruoyu Li Sheng Wang Feiyun Zhu Junzhou Huang GNN 230 817 0 10 Jan 2018
Unsupervised learning of dynamical and molecular similarity using variance minimization B. Husic Vijay S. Pande DRL 58 4 0 20 Dec 2017
Metadynamics for Training Neural Network Model Chemistries: a Competitive AssessmentJournal of Chemical Physics (JCP), 2017 John E. Herr Kun Yao R. McIntyre David W Toth John A. Parkhill 109 65 0 19 Dec 2017
Development and evaluation of a deep learning model for protein-ligand binding affinity prediction Marta M. Stepniewska-Dziubinska P. Zielenkiewicz P. Siedlecki 128 479 0 19 Dec 2017
A trans-disciplinary review of deep learning research for water resources scientists Chaopeng Shen AI4CE 427 799 0 06 Dec 2017