Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

Huang, Sheng-You, Grinter, Sam Z., Zou, Xiaoqin·2010·Physical Chemistry Chemical Physics

Cited by (513)

Items 401–500 of 513

  1. Forecasting maize yield from growth parameters using machine learning in a biochar-inorganic fertilizer amended soil under drip irrigation
    Oluwaseun Temitope Faloye, Ayodele Ebenezer Ajayi, Viroon Kamchoom‬, Natdanai Sinsamutpadung, Oluwafemi E. Adeyeri, Joshua Olalekan Ogunwole · 2025 · Smart Agricultural Technology
  2. Design, synthesis and exploration of cyclic imides as PDE4 inhibitors in psoriasis
    Veena K S, Pallabi Panja, Tirtha Nath, V.G.M. Naidu, Kalyan Kumar Sethi · 2026 · RSC Medicinal Chemistry
  3. DTAP: a unified graph transformer framework for joint prediction of drug–target affinity and docking pose
    Jiayi Liu, Yulian Ding, Yan Yan, Liangzhen Zheng, Yi Pan · 2026 · Briefings in Bioinformatics
  4. AI-driven multi-scale target analysis of traditional Chinese medicine: From the pharmacological effects of single compounds to the synergistic mechanisms of formulae
    Liang Hong, Muyao Teng, Min He, Jing Zhao, Shaoping Li · 2026 · Journal of Advanced Research
  5. Reviewing the Computational Landscape of Drug Repurposing: Evolution from Structure-Based Methods to LLM-Based Methods
    Ze-Yu Mou, Zhiqing Tian, Jiaqi Jin, Heng Yu, Yong-Zhen Huang · 2026 · Biomolecules
  6. Old drugs, new weapons: current trends in repurposing therapies against antimicrobial resistance
    Srikanth Gatadi, Niggula Praveen Kumar, Bhima Sridevi, Padma Bhavani Borra, Parul Thapar, Aabid Wani · 2026 · Journal of Pharmacy & Pharmaceutical Sciences
  7. A Machine Learning Approach to Enhance Scoring Performance in Docking-Based Virtual Screening Experiments: COX-1 as a Case Study.
    Cândida G. Silva, Pedro Carreiras, Elsa S. Henriques, Carlos J. V. Simões, Rui M. M. Brito · 2014 · IWBBIO
  8. Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates
    Nikola Minovski, Marjana Novič · 2015 · Advances in chemical and materials engineering book series
  9. Docking Methodologies and Recent Advances
    Ashwani Kumar, Ruchika Goyal, Sandeep Jain · 2016 · IGI Global eBooks
  10. Role of Molecular Docking in Computer-Aided Drug Design and Development
    Rahul Agarwal, Ashutosh Singh, Subhabrata Sen · 2016 · IGI Global eBooks
  11. FSDscore: An Effective Target‐focused Scoring Criterion for Virtual Screening
    Yi Hua, Dingfang Huang, Li Liang, Qian Xu, Xiaowen Dai, Yuan Xu, Haodi Qiu, Tao Lu, Haichun Liu, Yadong Chen et al. · 2022 · Molecular Informatics
  12. Reinforcement learning: A novel approach towards drug discovery
    Nishath Ansari, Amjan Shaik, Harika Patluri, Boga Varasree, K. Purnachand, Saikumar Tara · 2023 · AIP conference proceedings
  13. Free Energy Estimation for Drug Discovery: Background and Perspectives
    Fernando Daniel Prieto-Martínez, Yelzyn Galván-Ciprés · 2023 · BENTHAM SCIENCE PUBLISHERS eBooks
  14. Computational Toxicology Studies of Chemical Compounds Released from Firecrackers
    Alfred J. Lawrence, Nikita Tiwari, Tahmeena Khan · 2023 · BENTHAM SCIENCE PUBLISHERS eBooks
  15. Bacterial microbiome associated with cigarette beetle Lasioderma serricorne (F.) and its microbial plasticity in relation to diet sources
    Thanga Suja Srinivasan, Krishnamanikumar Premachandran, Paul X. Clinton · 2024 · PLoS ONE
  16. Traditional and machine learning approaches in structure-based drug virtual screening
    Hong Zhang, Yi Qin Gao · 2024 · Chinese Journal of Chemical Physics
  17. Biostatistical Investigation Using Docking Mechanism and Its Database to Investigate Drug Design, Drug Discovery, Drug Metabolism and Prediction Via Drug–Drug Interactions
    Ishika Gulati, Smriti Tripathi, Sachin Suresh Tiwari · 2024 · Springer eBooks
  18. Diterpene alcohol fraction of Cyperus rotundus Linn essential oil regulates Bcl-2 and Bax expression inducing apoptosis on HeLa in vitro and in silico
    Susianti Susianti, Yanwirasti Yanwirasti, Eryati Darwin, Jamsari Jamsari, Arif Setiawansyah · 2024 · Journal of Applied Pharmaceutical Science
  19. Challenges and Opportunities for Analyzing Protein–Ligand Interactions
    Saranya Arumugam, R. Muthuvel, C. Anjugam, Langeswaran Kulanthaivel, Gowtham Kumar Subbaraj · 2024 · Springer eBooks
  20. Chromatographic retention assisted in-silico prediction of anticancer potential of glucocorticoids on cancer cell lines
    Faten Farouk, Marwa M. Sharaky, Ehab Farouk Elkady, Rawda M. Sayed · 2025 · Journal of Chromatography B
  21. Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening
    Andreas Vitalis, David Parker, Fabian Radler, Pablo Andrés Vargas-Rosales, Yang Zhang, Jean‐Rémy Marchand, Amedeo Caflisch · 2025 · Journal of Computational Chemistry
  22. Computational Methods and Tools for Repurposing of Drugs Against Coronaviruses
    Sohini Chakraborti, Sneha Bheemireddy, Narayanaswamy Srinivasan · 2021 · Methods in pharmacology and toxicology
  23. Computational Approaches for Structure Based Drug Design and Protein Structure-Function Prediction
    Sai Lakshmana Vankayala · 2013 · Digital Commons - University of South Florida (University of South Florida)
  24. The Comparison of Docking Search Algorithms and Scoring Functions
    Marjana Novič, Tjaša Tibaut, Marko Anderluh, Jure Borišek, Tihomir Tomašič · 2016 · IGI Global eBooks
  25. Protein‐Ligand Docking
    Inna Slynko, Didier Rognan, Esther Kellenberger · 2017
  26. Benchmarking ensemble docking methods as a scientific outreach project
    Jessie L. Gan, Dhruv Kumar, Cynthia Chen, Bryn C. Taylor, Benjamin R. Jagger, R. Amaro, Christopher T. Lee · 2020 · bioRxiv
  27. In Silico Design and Selection of CD44 Antagonists
    Angel Jonathan Ruiz-Moreno · 2021
  28. FLEXIBLE TOPOLOGY: A NEW METHOD FOR DYNAMIC DRUG DESIGN
    Nazanin Donyapour, Nicole M. Roussey, Samik Bose, Alex Dickson · 2022 · ChemRxiv
  29. Theoretical and computational modeling of rna-ligand interactions
    Yuanzhe Zhou · 2021
  30. Virtual Screening and Bioactivity Modeling for G Protein‐Coupled Receptors
    Wallace K. B. Chan, Jiansheng Wu, Eric W. Bell, Yang Zhang · 2022 · Wiley eBooks
  31. Molecular Modeling and Simulation of Membrane Transport Proteins
    Andreas Jurik, Freya Klepsch, Barbara Zdrazil · 2012 · InTech eBooks
  32. Métodos de inteligencia artificial aplicados a química computacional en entornos de computación de alto rendimiento
    Cano Esquibel, José Gaspar · 2014
  33. On the estimation of ligand binding affinities
    Samuel Genheden · 2012 · Lund University Publications (Lund University)
  34. Study of interaction between polyphenolic compounds and protein using computational and capillary electrophoresis techniques
    Myalowenkosi Innocent Sabela · 2013
  35. CSCORE: A SIMPLE YET EFFECTIVE SCORING FUNCTION
    Xuchang Ouyang, Stephanus Daniel Handoko, Chee Keong Kwoh · 2011
  36. In silico drug discovery targeting Chikungunya virus
    Phuong T. V. Nguyen · 2015 · Research Online (University of Wollongong)
  37. Comparison of Cutoff Strategies for Geometrical Features in Machine Learning-Based Scoring Functions
    Shirley W. I. Siu, Thomas K. F. Wong, Simon James Fong · 2013 · Lecture notes in computer science
  38. In Silico-Guided Design of Novel-Scaffold Therapeutics Targeting the Dopamine D3 Receptor
    Debesai Gaim Hailemicael · 2014
  39. Novel strategies for wound treatment
    Mar Soe Win · 2013
  40. Studies of an ortho- Formylation Reaction and its Application for the Syntheses of Anti-Cancer Agents
    Øyvind W. Akselsen · 2011 · NORA - Norwegian Open Research Archives
  41. Docking Methodologies and Recent Advances
    Ashwani Kumar, Ruchika Goyal, Sandeep Jain · 2016 · Advances in medical technologies and clinical practice book series
  42. Identifying the Role of His293 in Protein Arginine Methyltransferase 1 and Characterization of Agonists for Peroxisomal Proliferator Activating Receptors
    Brittany Boykin · 2016
  43. Step IIIa: Biological Hit Discovery Through High-Throughput Screening (HTS): Random Approaches and Rational Design
    Pierfausto Seneci · 2018 · Elsevier eBooks
  44. Improving Protein-Ligand Docking by Particle Swarm Optimization
    Chon Kit Ng · 2014
  45. Screening and evaluation of natural compounds for therapeutic application in Alzheimer's disease
    Somashekara Nirvanashetty · 2024 · Swinburne figshare (Swinburne University of Technology)
  46. Métodos híbridos em docagem molecular: implementação, validação e aplicação
    Heloisa dos Santos Muniz · 2018
  47. Progesterone receptor ligand binding domain : from conformational dynamics to drug discovery
    Liangzhen Zheng · 2019
  48. CBSF: A New Empirical Scoring Function for Docking Parameterized by Weights of Neural Network
    Raulia R. Syrlybaeva, Marat R. Talipov · 2019 · Computational and Mathematical Biophysics
  49. Drug Repurposing for COVID-19 Using Molecular Docking Tools
    Deniz Yaşar Öztaş · 2021 · Chapman University Digital Commons (Chapman University)
  50. Predicting the structure and energetics of protein-ligand interaction
    Zhiwei Ma · 2019
  51. Production of Bioactive Compounds vs. Recombinant Proteins
    Maria F. Salazar Affonso, Débora Bublitz Anton, Daniel Kuhn, Bruno Rampanelli Dahmer, Camile Wünsch, Verônica Contini, Luís Fernando Saraiva Macedo Timmers, Cláucia Fernanda Volken de Souza, Márcia Inês Goettert, Rodrigo Gay Ducati · 2021
  52. Molecular Docking at a Glance
    Maryam Hamzeh‐Mivehroud, Babak Sokouti, Siavoush Dastmalchi · 2016 · IGI Global eBooks
  53. Scoring Functions of Protein-Ligand Interactions
    Zhiqiang Yan, Jin Wang · 2016 · IGI Global eBooks
  54. Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates
    Nikola Minovski, Marjana Novič · 2016 · IGI Global eBooks
  55. Aging and Alzheimer’s Disease
    Ruixue Ai, Xurui Jin, Bowen Tang, Guang Yang, Zhangming Niu, Evandro Fei Fang · 2022 · Springer eBooks
  56. Computer-Aided Drug Design for Membrane Channel Proteins
    Sören Wacker · 2012
  57. Molecular Docking of 2-[(morpholin-4-yl) (pyridin-3-yl) Methyl] Hydrazinecarboxamide (mph) Against Extended Spectrum of Beta Lactamase Enzyme Inhibition
    S Farook Basha, Angamuthu Raja, M. Syed Ali Padusha · 2018 · Research Journal of Life Sciences Bioinformatics Pharmaceutical and Chemical Sciences
  58. Virtual screening techniques in pharmaceutical research
    Justine C. Williams, Stanley K. A. Opare, Senthil Kumar Sugadoss, Aravindhan Ganesan, Subha Kalyaanamoorthy · 2022 · Elsevier eBooks
  59. Direct Determination of Pyrethroids in Aqueous Samples by a Metal Organic Framework “MIL-101(Cr)” Sorbent for Solid-Phase Extraction and Thermal Desorption Coupled with GC-FID
    Mahsa Torabizadeh, Kourosh Tabar Heydar, Seyyed Hamid Ahmadi · 2022 · Journal of Analytical Chemistry
  60. 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
  61. Algorithm Selection for Protein-Ligand Docking: A Case Study on ACE with AutoDock
    Tianlai Chen, Huiyuan Zhou, Xiwen Shu, Floyd A. Beckford, Mustafa Mısır · 2022 · ChemRxiv
  62. Virtual Screening of Kinase Based Drugs: Statistical Learning Towards Drug Repositioning
    M.T. Mustapha, Darren R. Flower, Amit Kumar Chattopadhyay · 2022 · Journal of Nanotechnology in Diagnosis and Treatment
  63. Molecular Docking of Michelia alba Leaves Active Compounds Against Human Epidermal Growth Factor Receptor 2 (HER-2)
    Felysia Isman, Paundra Pratama, Arif Fadlan · 2022 · Al-Kimia
  64. Retrieving Functional Pathways of Biomolecules from Single-Particle Snapshots
    Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben-Hail, Salah Salah, Peter Schwander, Amédée des Georges, Abhishek Singharoy, Joachim Frank, A. Ourmazd · 2023
  65. Estimation of binding free energies with Monte Carlo atomistic simulations and enhanced sampling
    Joan F. Gilabert · 2020
  66. Importance of In silico Tools in Anticancer Drug Discovery from Nature
    Gnana Ruba Priya Muthaiah, MVNL Chaitanya, Seema Sajjan Singh Rathore, Maida Engels S.E., Vishnu Nayak Badavath · 2023 · BENTHAM SCIENCE PUBLISHERS eBooks
  67. Molecular dynamics simulation study on the binding mechanism between carbon nanotubes and RNA-dependent RNA polymerase
    Zhaopeng Ma, Jianqiang Xu, Chenchen Wang, Zhicong Liu, Guanglai Zhu · 2024 · Journal of Biomolecular Structure and Dynamics
  68. ACOPLAMIENTO MOLECULAR. UNA BREVE REVISIÓN A LOS AVANCES RECIENTES SOBRE CÁNCER
    Diego Ramírez-Contreras · 2022 · RD-ICUAP
  69. Drugs targeting microRNAs that regulate DNA damage sensing and repair mechanisms: A computational drug discovery approach
    Bilachi S. Ravindranath, S. Vratin, B.S. Lakshmi, Darío C. Ramírez, Sandra Gomez-Mejiba · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  70. Improving the accuracy of pose prediction by incorporating symmetry-related molecules
    Sree Hima, Chandran Remya, K.V. Dileep · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Quantitative Structure Interaction Activity Relationship (QSIAR) as a Novel Approach to Drug Design: A Case Study of Anti-tubercular Agents
    Anil Kumar Saxena · 2024 · Springer eBooks
  72. Modeling protein flexibility in molecular docking
    Abeeb Ajibade, A. Liu, Xiaoqin Zou · 2025 · Elsevier eBooks
  73. RNA–Ligand Molecular Docking
    Phei Er Saw, Erwei Song · 2025 · Springer eBooks
  74. Retrospective Benchmarking and Novel Shape-Pharmacophore Based Implementation of the MORLD Method for the Autonomous Optimization of 3-Aroyl-1,4-diarylpyrroles (ARDAP)
    Pietro Sciò, Marianna Bufano, Romano Silvestri, Antonio Coluccia · 2025 · Journal of Chemical Information and Modeling
  75. Differential Evolution for Docking Simulations
    Amauri Duarte da Silva, Silvana Russo, Enrique González Vergara, Walter Filgueira de Azevedo · 2025 · Methods in molecular biology
  76. Molecular Docking Analysis Of Small Fullerene (C20, C22, C24) Nanoparticles With Lung (1X2J) And Breast (3HY3) Cancer Target Proteins
    Saadet Kaya · 2025 · Turkish computational and theoretical chemistry/Turkish computational and theoretical chemistry :
  77. Plant protein–ligand interactions: Interaction mechanism, binding forces, measuring, and overall features
    Ramy M. Khoder, Tao Yin, Nayyar Iqbal, Mohamed K. Morsy, Ibrahim Khalifa · 2025 · Elsevier eBooks
  78. Enzymes as Targets for Disease Control: From Discovery to Application
    Beatriz Brambila, Ana Carolina Franco Severo Martelli, Ana Elisa Moraes Rosa, Mariana Pegrucci Barcelos, Solange Cristina Antão, André Vessoni Alexandrino, Carlos Henrique Tomich de Paula da Silva, Maria Teresa Marques Novo‐Mansur · 2025 · Series in bioengineering
  79. 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
  80. Additional file 1 of SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors
    surendra kumar, Kim, Mi-hyun · 2021 · Figshare
  81. Additional file 1 of Structure-based, deep-learning models for protein-ligand binding affinity prediction
    Wang, Debby D., Wenhui Wu, Wang, Ran · 2024 · Figshare
  82. Strategies in the Discovery of Dual TRPA1‐PDE4B Inhibitors Against Psoriasis
    Veena K S, Meshram Nikhil Murtikumar, Kusal Gurung, Kalyan Kumar Sethi · 2025 · ChemistrySelect
  83. 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
  84. Application of Semiempirical Quantum Mechanical Methods To Accurately Estimate Ligand-Binding Structure in Biological Systems: Protein Kinase Case Study
    Charles‐Alexandre Mattelaer, Roberto Fino, Christian Permann, Thierry Langer, Edgar Jacoby, Jeremy Noel Harvey · 2026 · Journal of Chemical Information and Modeling
  85. Olive (Olea europaea) phenolics for the control of psoriasis via targeting SMYD2 and IL-17A protein–protein interaction networks
    Md Ashiq Mahmud, Mohamed M. Mohyeldin, Md. Towhidul Islam Tarun, Abu Bakar Siddique, Sitanshu S. Singh, Khalid A. El Sayed · 2026 · Journal of Natural Medicines
  86. Evaluating AlphaFold Tools and Related Scoring Functions for Protein–peptide Complex Prediction
    Negin Manshour, Jarett Zida Ren, Farzaneh Esmaili, Erik Bergstrom, Dong Xu · 2026 · Genomics Proteomics & Bioinformatics
  87. Recherche d'inhibiteurs de l'interaction Lutheran-Laminine par des techniques de modélisation et de simulation moléculaires
    Noelly Madeleine · 2017
  88. Computational approaches to molecular recognition : from host-guest to protein-ligand binding
    Joel José Montalvo‐Acosta · 2018 · theses.fr (ABES)
  89. Innovative inhibition strategy against functional structural transitions of essential pathogenic factors : Computational applications to Malarial and Neurotransmitter targets
    Laura Ortega Varga · 2019 · theses.fr (ABES)
  90. Development of force field methods
    Anastasia Croitoru · 2022
  91. Conception rationnelle de S-Glycosyltransférases issues d'Arabidopsis thaliana à façon : de la modélisation aux applications thérapeutiques et cosmétiques
    Damien Bretagne · 2022
  92. Distribution-preserved sampling (DPS) for smarter machine learning assisted ultra-large-scale virtual screening
    Alexander Trachtenberg, Alexander Spelkov, Barak Akabayov · 2026 · RSC Advances
  93. Inhibiting NHEJ: In-Silico Approach to Stratifying DNA-PK Inhibitors, Predicting Radio-Halogenation Potential of DNA-PK Inhibitors, and Assessing AlphaFold2 Prediction Accuracy
    Dragoș Andrei Niculae, Florin-Vlad-Gabriel Crișu, Sabin Stoian, Daniel Ion, Doina Drăgănescu · 2026 · Bioengineering
  94. Allosteric Interactions of Flavonoids with ACE2 and Potential Implications for COVID-19: Computational Insights, Metabolic and Mitochondrial Effects of Rutin in A549 Cells
    Fave Yohanna Tata, Mthokozisi Bongani Nxumalo, Vincent A. Obakachi, Hezekiel Mathambo Kumalo, Rene Bernadette Khan · 2026 · Cell Biochemistry and Biophysics
  95. Docking in cancer, neurological disorders, and infectious diseases
    Mohd Faizan Siddiqui, Azaroual Mouna, Калматов Роман Калматович, Gulnara Isaeva, Kudaiberdieva Gulmira Karimovna, Gulzat Gapyrova Maksatbekovna, Paizova Mamazakirovna, Anara Keneshovna Zhanbaeva, Imetova Jazgul Bukarbaevna, Ainura Zarylbekovna Kutmanova et al. · 2026 · Elsevier eBooks
  96. Molecular docking workflows and pipelines
    Kamalika Dhar, Debabani Ganguly · 2026 · Elsevier eBooks
  97. Improving high-degree-polymerization GOS synthesis of a marine cold-active β-galactosidase via semi-rational design
    Pan, Lin, Zhang, Yali, Wang, Zhe, Fan, Chenxu, You, Qionghui, Wu, Jiahong, Feng, Fangqi, Wang, Xiaohui · 2026 · Archives of Microbiology
  98. Exploring thiazole conjugates as cholinesterase inhibitors for Alzheimer’s disease treatment
    Anchal Dabas, Praduman Yadav, Ram Singh · 2026 · Future Medicinal Chemistry
  99. Deep generative models for 3D structure-based drug design and molecular optimisation: a comprehensive survey
    Y Zhang, Yuyouqiang Fu, Guishen Wang · 2026 · Journal of Computer-Aided Molecular Design
  100. Graph-based drug–target interaction modeling: from representation learning to output-driven drug discovery
    Thành Nguyen, Hiến Minh Tô, Duy Anh Nguyen, Duy Trieu, Giang Nguyen · 2026 · Briefings in Bioinformatics