Application advances of deep learning methods for de novo drug design and molecular dynamics simulation

Bai, Qifeng, Liu, Shuo, Tian, Yanan, Xu, Tingyang, Banegas‐Luna, Antonio Jesús, Pérez‐Sánchez, Horacio, Huang, Junzhou, Liu, Huanxiang +1 more·2022·WIREs Computational Molecular Science
DOI 10.1002/wcms.1581

Cited by (156)

Items 101–156 of 156

  1. Computational Approaches for the Inhibition of ESKAPE Pathogens
    Subhaswaraj Pattnaik, Monika Mishra, Pradeep Kumar Naik · 2024 · Springer eBooks
  2. Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats
    Wei Chen, Yihui Ren, Ai Kagawa, Matthew R. Carbone, Samuel Yen-Chi Chen, Xiaohui Qu, Shinjae Yoo, Austin Clyde, Arvind Ramanathan, Rick L. Stevens et al. · 2023 · International Conference on Machine Learning and Applications
  3. Future Trends and Challenges in Pharmaceutical Microbiology with the Integration of Artificial Intelligence
    Tarun Kumar Vashishth, Vikas Sharma, Kewal Krishan Sharma, Sanjukta Vidyant, Abhay Bhardwaj · 2024 · Advances in medical technologies and clinical practice book series
  4. PDL1-inhi.predictor: a two-tiered machine learning framework for predicting and prioritizing PDL1 inhibitors
    Huiyan Ying, Junting Liu, Weikaixin Kong, Xiangwei Xu · 2025 · Bioorganic Chemistry
  5. A review of recent advances in generative artificial intelligence models for biomolecular sciences
    Jian Jiang, Daixin Li, Guilin Wang, Nicole Hayes, Ya-Zhou Shi, Huahai Qiu, Bengong Zhang, Tianshou Zhou, Guo‐Wei Wei · 2025 · Acta Pharmaceutica Sinica B
  6. HVLGAN: hybrid hierarchical scaled attention-enabled latent model for structure-based drug discovery
    Shreyas Rajendra Hole, M Lakshmanan, R Jeevaraj, Manumula Srinubabu, Shreekant Salotagi, Vinothkumar Kolluru · 2026 · Journal of Biomolecular Structure and Dynamics
  7. Integrated network pharmacology, molecular docking, and experimental validation reveal synergistic inhibition of EGFR and PI3K-Akt/JAK2-STAT3 pathways by Esculin and Esculetin to exert anti-colorectal cancer effects
    Liao Lin, Zhaohui Tang, Pengfei Luo, Ruoting Tang, Hanzhi Li, Guangliang He, Jianjin Guo, Sijuan Ding · 2026 · Toxicology and Applied Pharmacology
  8. Vir2Drug: a drug repurposing framework based on protein similarities between pathogens
    George Minadakis, Marios Tomazou, Nikolas Dietis, George M. Spyrou · 2022 · Briefings in Bioinformatics
  9. Optimization of binding affinities in chemical space with generative pre-trained transformer and deep reinforcement learning
    Xiaopeng Xu, Juexiao Zhou, Chen Zhu, Qing Zhan, Zhongxiao Li, Ruochi Zhang, Yu Wang, Xingyu Liao, Xin Gao · 2024 · F1000Research
  10. Probing the interaction between the metallo‐β‐lactamase SMB ‐1 and ampicillin by multispectral approaches combined with molecular dynamics
    Jiachen Li, Xiaoting Dong, Yeli Zhang · 2024 · Journal of Molecular Recognition
  11. Identify Regioselective Residues of Ginsenoside Hydrolases by Graph-Based Active Learning from Molecular Dynamics
    Yi Li, Hong-Qian Peng, Meng‐Liang Wen, Li-Quan Yang · 2024 · Molecules
  12. Interaction of Twenty-Seven Bicyclo Derivatives with VEGF Receptors as a Therapeutic Alternative to Treat Cancer
    López‐Ramos Maria, Lauro Figueroa-Valverde, Rosas‐Nexticapa Marcela, Magdalena Alvarez-Ramirez, Virginia Mateu-Armand, Cauich-Carrillo Regina · 2024 · Clinical Cancer Investigation Journal
  13. A spatial-temporal graph attention network for protein–ligand binding affinity prediction based on molecular geometry
    Gai‐Li Li, Yongna Yuan, Ruisheng Zhang · 2025 · Multimedia Systems
  14. Deep Learning Reaction Framework (DLRN) for kinetic modeling of time-resolved data
    Nicolò Alagna, Brigitta Dúzs, Vincent Dietrich, Ali Tayefeh Younesi, Livia Lehmann, Ronald Ulbricht, Heinz Koeppl, Andreas Walther, Susanne Gerber · 2025 · Communications Chemistry
  15. Contrastive learning-based drug screening model for GluN1/GluN3A inhibitors
    Kun Li, Yue Zeng, Yi-Da Xiong, Hao-chen Wu, Sui Fang, Zhi-yan Qu, Yan Zhu, Bo Du, Zhao-Bing Gao, Wen-Bin Hu · 2025 · Acta Pharmacologica Sinica
  16. O impacto da inteligência artificial nas ciências da vida através da bioinformática
    Lucas Moraes dos Santos, Diego Mariano, Raquel C. de Melo-Minardi · 2023 · Revista da Universidade Federal de Minas Gerais
  17. Structure and dynamics of 5-lipoxygenase and its complexes — a molecular dynamics simulation study
    Shahid Duran, Syed Tarique Moin · 2023 · Journal of Molecular Modeling
  18. Explaining structure-activity relationships using locally faithful surrogate models
    Heta A. Gandhi, Andrew Dickson White · 2022 · ChemRxiv
  19. Recent Knowledge in Drug Design and Development: Automation and Advancement
    Kusum Gurung, Saurav Kumar Mishra, Tabsum Chhetri, Sneha Roy, Anagha Balakrishnan, John J. Georrge · 2025
  20. Deep reinforcement learning in drug design
    Hao Lu, Qian Wang, Kun Zhang, Zirong Huang, Xiancong Hou, Guohui Zhao, Hao Liu · 2025 · Elsevier eBooks
  21. Diabetic Retinopathy Detection with Uncertainty scores: A Combined Approach Using Transfer Learning and Ensemble Calibration
    Preeti Verma, Sivasankar Elango, Kunwar Singh · 2025 · ADCAIJ ADVANCES IN DISTRIBUTED COMPUTING AND ARTIFICIAL INTELLIGENCE JOURNAL
  22. Harnessing artificial intelligence in healthcare: Advancing diagnosis, treatment, and patient-centered care
    Amiya Das, Deepshi Arora, Geeta Deswal, Ajmer Singh Grewal, Shilpi Bansal · 2026 · Journal of the National Medical Association
  23. Structure‐Based Virtual Screening of Propolis‐Derived Compounds as Quorum Sensing Inhibitors in Stenotrophomonas maltophilia Using Molecular Docking and Dynamics Simulations
    Fettouma Chraa, Doha EL Meskini, Abdelhakim Bouyahya, Gokhan Zengn, Rachid EL Jaoudi, Mouna Ouadghiri, Tarik Aanniz · 2026 · ChemistrySelect
  24. Integrative Computational Strategies for Dynamic GPCR Landscapes: From Conformational Mechanisms to Drug Design
    Jieying Zang, Shihang Wang, Kai Xu, Xinke Zhan, Yanan Tian, Xiaojun Yao, Huanxiang Liu · 2026 · Wiley Interdisciplinary Reviews Computational Molecular Science
  25. Enhancing the Efficiency of Medicinal Chemistry Through Computational Chemistry
    Toahira Eakin, Jannatul Ferdaous, Sajjad Hossain, Jannatul Ferdous, Sarkar M. A. Kawsar · 2025 · IGI Global eBooks
  26. Revolutionizing Scientific Research
    Andi Asrifan, Sajed S. Ingilan · 2025 · Advances in computational intelligence and robotics book series
  27. ENERGIAS LIVRES DE LIGAÇÃO ABSOLUTA DO PEPTÍDEO ANTIVIRAL ATN-161 COM ALVOS PROTEICOS DE SARS-COV-2
    RUDIELSON DOS SANTOS SILVA · 2023
  28. Molecular Dynamics Simulation by Implementing Parallel Computing and Big Data Principles
    Debangan Mandal, Kumar A. Shukla, Aditya Ghosh · 2023 · IEEE IAS Global Conference on Emerging Technologies (GlobConET)
  29. Machine Learning in Molecular Dynamics Simulation
    Xiaojing Teng · 2023 · Lecture notes in electrical engineering
  30. Synthesis and study of the hemostatic activity of substituted 5-oxo-1-cyano-3-{(3-cyano-4,5,6,7tetrahydrobenzo[b]thiophen-2-yl)amino{penta-1,3-dien-2-olate potassium
    Dmitriy V. Lipin, D. A. Kozlov, V. M. Shadrin, K. Yu. Parkoma, A. V. Starkov, Daria A. Shipilovskikh, Н. А. Пулина, Sergei Alexandrovich Shipilovskikh · 2023 · Журнал органической химии
  31. Decyclization of substituted 3-(4-nitrobenzoyl)hydrasono3H-furan-2-ones under the action of primary alcohols and investigation of analgesic activity and acute toxicity of reaction products
    Dmitriy V. Lipin, E. I. Denisova, Daria A. Shipilovskikh, Рамиз Рагибович Махмудов, Назим Мусабекович Игидов, Sergei Alexandrovich Shipilovskikh · 2023 · Журнал органической химии
  32. An Optimization Method for Drug Design Based on Molecular Features
    Xuan Liu, Xiaoli Lin, Fengli Zhou · 2024 · Lecture notes in computer science
  33. Deep Learning Reaction Network: a machine learning framework for modeling time resolved data
    Nicolò Alagna, Brigitta Dúzs, Heinz Koeppl, Andreas Walther, Susanne Gerber · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  34. Elucidation of Molecular Substructures from Nuclear Magnetic Resonance Spectra Using Gradient Boosting
    Josef Berman, Yehudit Aperstein, Abraham Yosipof · 2024 · Lecture notes in computer science
  35. Synthesis and Analgesic Activity of Substituted N-Alkyl-4-aryl-2-aroylhydrazylidene-4-oxobutanamides
    E. I. Denisova, Olesya V. Zvereva, Dmitriy V. Lipin, Рамиз Рагибович Махмудов, Илья Николаевич Чернов, Екатерина Сергеевна Денисламова, Daria A. Shipilovskikh, Назим Мусабекович Игидов · 2024 · Russian Journal of Organic Chemistry
  36. Computational Approaches in Drug Design
    Sajjad Hossain, Jannatul Ferdaous, Toahira Eakin · 2025 · IGI Global eBooks
  37. Impact of Medical Information Science on Drug Discovery and Pharmaceutical Data Management
    Kollathur Sudheer, Paramjit Baxi, Jaspreet Sidhu, Keshav Keshav, K. Jamuna, Zuleika Homavazir, Pratap Kumar Sahu · 2024 · Seminars in Medical Writing and Education
  38. Synthesis and Study of Antimicrobial Activity of Reaction Products of Substituted 3-Thienylimino-3H-furan-2-ones with Substituted Hydrazines and Hydrazides
    Dmitriy V. Lipin, Н. А. Пулина, Валентина Васильевна Новикова, Рамиз Рагибович Махмудов, N. V. Zhekina, V. M. Shadrin · 2025 · Russian Journal of General Chemistry
  39. Artificial Intelligence in Pharmaceutical Drug Development-challenges and the Way Forward
    Venkateshwaran Krishnaswami, Selvakumar Muruganantham, Jacob Raja, Saravanakumar Arthanari, Brito Raj Selvaraj, Jose Prakash Dharmian · 2025 · Current Artificial Intelligence
  40. Synthesis and study of anti-inflammatory activity of N-alkyl-2-aroylhydrazinylidene-4-oxobutanamides
    E. I. Denisova, Olesya V. Zvereva, Dmitriy V. Lipin, Светлана Викторовна Чащина, Илья Николаевич Чернов, Екатерина Сергеевна Денисламова, Daria A. Shipilovskikh, Назим Мусабекович Игидов · 2025 · Russian Chemical Bulletin
  41. Synthesis and antinociceptive activity of potassium 1-alkoxy-6-aryl-2-cyano-4-[(3-cyano-4,5,6,7-tetrahydrobenzo[b]-thiophen-2-yl)amino]-1,6-dioxohexa-2,4-dien-3-olates
    Dmitriy V. Lipin, V. M. Shadrin, S. K. Metlyakova, P. S. Silaichev, Рамиз Рагибович Махмудов, Daria A. Shipilovskikh · 2025 · Russian Chemical Bulletin
  42. Overcoming translational barriers in RNA–protein docking: enhancing computational accuracy for targeted drug discovery
    Habiba Akram, Muneeb Ur Rahman, Sharjeel Mazhar, Farheen Qamer, Ayesha Yousaf · 2025 · Future Medicinal Chemistry
  43. Advancements in Precision Oncology: Harnessing High-Throughput Screening and Computational Strategies for Targeted Cancer Therapies
    Akshay Thakur, Kakuli Chowdhury, Vir Vikram Sharma, Kuldeep Singh, Jeetendra Kumar Gupta, Divya Jain, Mukesh Chandra Sharma · 2025 · Combinatorial Chemistry & High Throughput Screening
  44. AI Data Applications in Drug Design, Development, and Diagnostics: A Comprehensive Approach to Modern Medicine
    Ritika Singh, Prasoon Pandey, Anuj Kumar, Manoj Kumar Mishra · 2025 · Current Bioinformatics
  45. A study on the impact of Deep Learning on de-aging the characters in movies between 2010–2024: A Systematic Review
    Manikandan C, Fakira Mohan Nahak · 2025 · International Conference on Circuits, Power and Intelligent Systems (CCPIS)
  46. Transforming healthcare technologies through the application of artificial intelligence and machine learning in pharmaceutical sciences
    Aisha Idris, Sithu Aung, Humaira Shah, Nelli Giribabu · 2025 · International Journal of Clinical Medical Research
  47. Validation Aspects in Structure-Based Drug Design
    Viet‐Khoa Tran‐Nguyen, Thai‐Son Tran, Phuong Thuy Viet Nguyen, Khac‐Minh Thai · 2025 · Springer handbooks
  48. Force Field Parameterization in Molecular Simulation by Machine Learning Methods
    Gong Chen · 2023 · theses.fr (ABES)
  49. Artificial intelligence for drug discovery and development
    Jassica, Jaspreet Singh Bajaj, Kimmi Gupta, Rajesh Kumar Kaushal, Naveen Kumar · 2026 · AIP conference proceedings
  50. Solidification intervention strategies for efficient encapsulation of water-soluble drugs via oil-in-water emulsion techniques
    Guangfei Wei, Meng Chen, Yang Yang, Shujing Qian, Zhongxing Li, Xun Sun, Zhirong Zhang, Tao Gong, Bin Zong, Qing Lin · 2026 · Journal of Controlled Release
  51. Oleanolic Acid Inhibits Acetylcholinesterase and Butyrylcholinesterase Through Gorge‐Dependent Allosteric Mechanisms: An Integrated Kinetic and Molecular Dynamics Study
    Ahmed M. Hakami, Fettouma Chraa, Doha EL Meskini, Hafiz Antar Makeen, Rym Hassani, Mohammed Albratty, Zia Ur Rehman, Abdelhakim Bouyahya, Tarik Aanniz · 2026 · Flavour and Fragrance Journal
  52. ZIF-8 Frameworks as Potential Controlled-Release Urea Fertilizers: Experimental and Computational Insights
    Rukiye Taş, Berna Burcu Topuz, Hakan Kayı · 2026 · ACS Agricultural Science & Technology
  53. Beyond the flat screen: evaluating virtual reality as a complementary tool for molecular docking in drug discovery
    Viktoria A. Feoktistova, Korney Aruko, Екатерина Владимировна Скорб, Sergey Shityakov · 2026 · Journal of Computer-Aided Molecular Design
  54. Position: Federated Learning for Proprietary Materials Databases — Privacy-Preserving Training without Centralized Data
    Samuel Boateng, Kwesi Mensah, Kojo Asante, Linda Owusu · 2025 · Journal of Computational and Data-Driven Materials Engineering
  55. Artificial Intelligence in Organic Synthesis
    Alexey А. Festa, Leonid G. Voskressensky, Matvey K. Shurikov, Павел Сергеевич Постников, Valentine P. Ananikov · 2026 · The Chemical Record
  56. A Memristive Hopfield Neural Network Driven by Electromagnetic Radiation for Dynamic Modeling of Molecular Interaction Patterns
    Anurag Sinha, Rupesh Mishra, Shrikant Burje, Surinder Kaur, Suryansh Rai, Saroj Kumar Pandey, Yogesh Kumar Rathore, Aseel Smerat, Md. Sazid Reza · 2026 · Journal of Electrical and Computer Engineering