Machine‐learning scoring functions to improve structure‐based binding affinity prediction and virtual screening

Cited by (357)

Items 301–357 of 357

1. Structure-Based Virtual Screening: Theory, Challenges and Guidelines
   Maria Kontoyianni · 2021 · Elsevier eBooks
2. Increasing the Accuracy of Optipharm’s Virtual Screening Predictions by Implementing Molecular Flexibility
   Savíns Puertas Martín, Juana L. Redondo, Ester Martín Garzón, Horacio Pérez‐Sánchez, Pilar M. Ortigosa · 2022 · Lecture notes in computer science
3. Enhancing structure-based virtual screening of MDM2–p53 inhibitors: a benchmark of machine learning vs. traditional docking scoring functions
   Marcia Yineth Castillo Tarazona, Gian Pietro Miscione · 2026 · Frontiers in Drug Discovery
4. Future Perspectives of Computational Drug Design
   Gisbert Schneider · 2018 · Wiley eBooks
5. Ollivier persistent Ricci curvature (OPRC) based molecular representation for drug design
   JunJie Wee, Kelin Xia · 2020 · arXiv (Cornell University)
6. A Hybrid Alchemical Free Energy and Machine Learning Methodology for the Calculation of Absolute Hydration Free Energies of Small Molecules
   Jenke Scheen, Wilson Wu, Antonia S. J. S. Mey, Paolo Tosco, Mark Mackey, Julien Michel · 2020 · ChemRxiv
7. Toward Out-of-Domain Binding Affinity Prediction
   Zehan Zhao, Shujun Fang, Haohan Wang · 2023 · Research Square
8. Community Benchmarking Exercises for Docking and Scoring
   Bharti Devi, Anurag T. K. Baidya, Rajnish Kumar · 2024
9. Protein Docking and Drug Design
   Aditi Gangopadhyay, Hirak Jyoti Chakraborty, Abhijit Datta · 2017 · Advances in bioinformatics and biomedical engineering book series
10. Progesterone receptor ligand binding domain : from conformational dynamics to drug discovery
    Liangzhen Zheng · 2019
11. Modeling Protein-Ligand Interactions: Are We Ready for Deep Learning?
    Didier Rognan · 2019 · Elsevier eBooks
12. Reposicionamento de fármacos para o tratamento da doença de Chagas: desenvolvimento de modelos computacionais baseados em ligantes ativos fenotipicamente contra o Trypanosoma cruzi e na inibição da diidroorotato desidrog
    Marcos Antonio Ferreira · 2021 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
13. Computational approaches to discover novel enzymes for fragrance and flavour
    Janani Durairaj · 2021
14. Faculty Opinions recommendation of Updates to binding MOAD (mother of all databases): polypharmacology tools and their utility in drug repurposing.
    Giulio Rastelli · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
15. Assessing the generalization abilities of machine-learning scoring functions for structure-based virtual screening
    Hui Zhu, Jincai Yang, Niu Huang · 2022 · ChemRxiv
16. Artificial Intelligence: As an innovative technique in healthcare sector and as a potent technique to fight against COVID-19
    Priya Pandey · 2022 · YMER Digital
17. ALGORITMO DE CLASIFICACIÓN MEDIANTE UN ENFOQUE DE MACHINE LEARNING Y SU APLICACIÓN AL ESTUDIO METEOROLÓGICO
    Pedro Elizardo Donis del Cid · 2022 · Journal of Engineering Research
18. Molecular Recognition and Machine Learning to Predict Protein‐Ligand Interactions
    A. Reyes Chaparro, J.A. Moreno‐Melendres, A.L. Ramos‐Jacques, A.R. Hernandez‐Martinez · 2022
19. Geometric and topological AI for molecular sciences
    JunJie Wee · 2023
20. A new protein-ligand docking software with an improved method of molecular conformation optimization
    Rafael Temirgaliev, Dmitry Pavlov · 2023 · ChemRxiv
21. Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors
    Klaudia Caba, Viet‐Khoa Tran‐Nguyen, Taufiq Rahman, Pedro J. Ballester · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
22. Virtual Screening Strategies in Drug Discovery: Potential Inhibitors of Candida Albicans Cytochrome B
    xi xu, Shuangkou Chen, Wanhong Zhu, Yu Tian Wang, Xia Huang, Xin Yang, Fengming Ren · 2024 · SSRN Electronic Journal
23. Virtual Screening Strategies in Drug Discovery: Potential Inhibitors of Candida Albicans Cytochrome B
    xi xu, Shuangkou Chen, Wanhong Zhu, Yu Wang, Xia Huang, Xin Yang, Fengming Ren · 2024 · SSRN Electronic Journal
24. Exploring the impact and applications of artificial intelligence in advancing modern medical diagnostic practices-role of healthcare providers
    Fahdah Mehsan Alotaibi, ‏Abdulrhman Ali Almazam, ‏Arwa Mohammad Emam, ‏Naif Saad Alqahtani, ‏Ashwaq Ibrahim Alheggi, ‏Waseem Nasser Alshahranl, ‏Ashwaq Fahad Alanazi, ‏Maryam Helal Alanazi, ‏Mahfoudh Saad Alghamdi, ‏Abdulaziz Shaem Alsharari et al. · 2020 · International Journal of Health Sciences
25. Extreme Gradient Boosting Beats In‐Silico Identification of Proteins Potentially Associated With Alzheimer’s
    Sadia Khalil, Wajid Arshad Abbasi, Syed Ali Abbas, Maryum Bibi, Saiqa Andleeb, Amsa Shabir · 2024 · Applied Computational Intelligence and Soft Computing
26. Computational Toxicology
    Jie Liu, Fan Dong, Wenjing Guo, Zoe Li, Weida Tong, Tucker A. Patterson, Huixiao Hong · 2024 · Elsevier eBooks
27. RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models
    Romanos Fasoulis, Γεώργιος Παλιούρας, Lydia E. Kavraki · 2024 · Journal of Chemical Information and Modeling
28. Affinity prediction using a neural network model for the m1 protein of group a streptococcus in customized medicine
    Chaitra Gajulla Nagaraja, Daisy Vanitha John, Pratham Tarachand Lalwani · 2025 · Journal of Nursing Research Patient Safety and Practise
29. Aptamer-Based Cancer Diagnosis: Emerging Updates
    Mithun Singh Rajput, Gopal Natesan · 2025 · Springer eBooks
30. Toward Out-of-Domain Binding Affinity Prediction
    Zehan Zhao, Shujun Fang · 2024 · International Conference on Universal Village (UV)
31. Network Pharmacology Integrated Molecular Docking‐Based Mechanistic Role of Phytobioactives in Autism Spectrum Disorder
    Rajnish Srivastava, Sonalika Bhalla, Pradeepta Kumar Sarangi, Ashok Kumar Sahoo, Dhriti Verma · 2025 · Macromolecular Symposia
32. Exploring promising pharmaceutical candidates for gastrointestinal disorders using In silico approaches
    R. D. Singh, Vaishali, Ravi Kumar Deshwal, Kopal Jain, Nikita Basant · 2025 · Elsevier eBooks
33. Additional file 1 of Learning protein-ligand binding affinity with atomic environment vectors
    Meli, Rocco, Andrew Anighoro, Mike J. Bodkin, Garrett M. Morris, Philip Charles Biggin · 2021 · Figshare
34. Additional file 1 of Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors
    Klaudia Caba, Viet‐Khoa Tran‐Nguyen, Rahman, Taufiq, Pedro J. Ballester · 2024 · Figshare
35. Additional file 1 of The impact of cross-docked poses on performance of machine learning classifier for protein–ligand binding pose prediction
    Shen, Chao, Hu, Xueping, Junbo Gao, Zhang, Xujun, Zhong, Haiyang, Wang, Zhe, Xu, Lei, Kang, Yu, Cao, Dongsheng, Tingjun Hou · 2021 · Figshare
36. Additional file 1 of GNINA 1.0: molecular docking with deep learning
    Andrew T. McNutt, Paul G. Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri, Koes, David Ryan · 2021 · Figshare
37. Additional file 1 of ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions
    Zhang, Xujun, Shen, Chao, Xueying Guo, Wang, Zhe, Gaoqi Weng, Qing Ye, Wang, Gaoang, He, Qiaojun, Yang, Bo, Cao, Dongsheng et al. · 2021 · Figshare
38. Additional file 1 of Antioxidant evaluation and computational prediction of prospective drug-like compounds from polyphenolic-rich extract of Hibiscus cannabinus L. seed as antidiabetic and neuroprotective targets: assessment through in vitro and in silico studies
    Afolabi, Olakunle Bamikole, Oluwaseun Ruth Olasehinde, Damilola Grace Olanipon, Samson Olatunde Mabayoje, Olufemi Michael Familua, Kikelomo Folake Jaiyesimi, Esther Kemi Agboola, Idowu, Tolulope Olajumoke, Obafemi, Olabisi Tajudeen, Oyindamola Adeniyi Olaoye et al. · 2023 · Figshare
39. Additional file 1 of TB-IECS: an accurate machine learning-based scoring function for virtual screening
    Zhang, Xujun, Shen, Chao, Jiang, Dejun, Zhang, Jintu, Ye, Qing, Xu, Lei, Tingjun Hou, Pan, Peichen, Yu Sung Kang · 2024 · Figshare
40. Small Molecule-Target Binding Affinity Prediction and Scoring Function Design
    Tingjun Hou · 2025 · Springer eBooks
41. SMARTDock: A Toolkit for the Automated Development of Target-Specific Scoring Functions Using Bioactivity Data
    Felipe Victoria-Muñoz, Norberto Sánchez‐Cruz, Oliver Koch · 2026 · Journal of Chemical Information and Modeling
42. 27Chapter 2 AI-based approaches to cancer drug discovery
    Rishabha Malviya, Shivam Rajput, Mukesh Roy, Sathvik Belagodu Sridhar, Sabin Thomas · 2025 · De Gruyter eBooks
43. Learning protein-ligand binding affinities through an uncertainty-aware attention mechanism
    Debby D. Wang, Tianlun Zhang, Xizhao Wang · 2025 · Conference proceedings/Conference proceedings - IEEE International Conference on Systems, Man, and Cybernetics
44. Development of efficient multiscale methods and extrapolation techniques for multiphysics molecular chemistry
    Étienne Polack · 2022
45. Design and application of deep learning methods to structure-based drug design
    Mikhail Volkov · 2023 · theses.fr (ABES)
46. Computational fragment-based design of chemically modified oligonucleotides for selective protein inhibition : BACE1 as a case study
    Roy González‐Alemán · 2023
47. ROCK2 Inhibition Underlying the Anticancer Effects of Dobutamine: A Novel Proposed Mechanism
    Safa Daoud, Alaa Abuawad, Rana Abu‐Dahab, Mutasem O. Taha · 2026 · The Open Medicinal Chemistry Journal
48. Physics-Informed Artificial Intelligence Design of Picomolar Nanobodies Enables Deep Tumor Penetration and High-Contrast Imaging
    Ning Shi, Caiping Ren, Liang Zhang, Lei Wang, Lei Wang, Xiaobo Li, Yangyihua Zhou, Jie Wang, Pinnan Zhao, Chaoyan Yao et al. · 2026 · Research
49. Molecular docking tools and their benchmarking: A practical guide for interdisciplinary researchers
    Bikash Kumar Rajak, Priyanka Rani · 2026 · Elsevier eBooks
50. How Bias Shapes the Leaderboard: Scoring Function Performance Under Scrutiny
    David Graber, Jakub Kopko, Peter Stockinger, Ravidu Nakandalage, Bernd Kuhn, Siddhartha Mishra · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
51. Native Contact Ratio as a Topological Metric for Machine Learning Based Molecular Docking
    Zhenqiang Zhang, Zhihao Wang, Yang Liu, Xiangdong Liu, Shicai Xu, Yanmei Yang, Yuanyuan Qu, Weifeng Li · 2026 · Journal of Chemical Information and Modeling
52. UniPoseScore: A Unified Graphormer3D-Based Framework for Protein–Ligand Binding Pose Scoring and Refinement
    Jinqiao Zhang, Xinyu Ren, Zhenling Peng, Hong Wei · 2026 · Journal of Chemical Information and Modeling
53. Natural Product‐Derived ErbB1 Inhibitors Identified Through Machine Learning‐Based QSAR, Molecular Docking, and Molecular Dynamics Simulations
    Fateh Bouchama, Abdelhafid Djerourou, Abdelmalek Khorief Nacereddine, Khairedine Kraim, Mohammed Brahimi, Youcef Saihi, Karima Mezghiche, Mutasem O. Taha · 2026 · ChemistrySelect
54. Development and Evaluation of Target-Specific Machine-Learning Scoring Functions for Monoamine Oxidase B
    Sherif A. Elsabbagh · 2026 · Research Square
55. An inverse-protein-folding pre-trained model for predicting the mutational effects in protein-protein interactions
    Sihong Mao, Siwei Meng, Ye Xiang · 2026 · iScience
56. Sequence-Driven Classification of Protein and Peptide Aptamer Targets Using TF-IDF Based Ensemble Models
    Ava George, Sahith Goli, Andrew Takayama, Andres Medina, Amanda Reyes, Damian Ventura, Stevan Pecic, Ankita Mohapatra · 2026 · International Conference on Advanced Machine Learning and Data Science (AMLDS)
57. DockBind: A Quality-Controlled Data Set of Modeled Protein–Ligand Complexes Associated with Affinity Data
    Alberto Rovetta, Alberto Memè, Hanne Antila, Ruth Brenk · 2026 · Journal of Chemical Information and Modeling