Binding MOAD (Mother Of All Databases)

Cited by (329)

Items 201–300 of 329

1. High Impact: The Role of Promiscuous Binding Sites in Polypharmacology
   Natacha Cerisier, Michel Petitjean, Leslie Regad, Quentin Bayard, Manon F. Réau, Anne Badel, Anne‐Claude Camproux · 2019 · Molecules
2. Virtual Screening
   A. C. Good · 2007 · Elsevier eBooks
3. Effect of Biomolecular Conformation on Docking Simulation: A Case Study on a Potent HIV-1 Protease Inhibitor.
   Nima Razzaghi‐Asl, Saghi Sepehri, Ahmad Ebadi, Ramin Miri, Sara Shahabipour · 2015 · Europe PMC (PubMed Central)
4. Molecular Modelling
   Xavier Barril, Robert Soliva · 2006 · Molecular BioSystems
5. Artificial Intelligence and Machine Learning Applications in Vaccine Development
   Ali Sarmadi, Majid Hassanzadeganroudsari, Mohsen Beikali Soltani · 2023
6. Variation of protein binding cavity volume and ligand volume in protein–ligand complexes
   Saranya Nallusamy, Samuel Selvaraj · 2009 · Bioorganic & Medicinal Chemistry Letters
7. Prediction of Water Distributions and Displacement at Protein–Ligand Interfaces
   Noam Morningstar-Kywi, Kaichen Wang, Thomas R. Asbell, Zhaohui Wang, Jason B. Giles, Jiawei Lai, Dab Brill, Brian T. Sutch, Ian S. Haworth · 2022 · Journal of Chemical Information and Modeling
8. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores
   Mark L. Benson, John C. Faver, Melek Nihan Ucisik, Danial Sabri Dashti, Zheng Zheng, Kenneth M. Merz · 2012 · Journal of Computer-Aided Molecular Design
9. Public Chemical Databases
   Sunghwan Kim · 2017 · Elsevier eBooks
10. Database of protein complexes with multivalent binding ability: Bival‐bind
    Tim Meyer, Ernst‐Walter Knapp · 2013 · Proteins Structure Function and Bioinformatics
11. Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment
    M. Lucrecia Bogado, Roxana Noelia Villafañe, José Leonardo Gómez Chávez, Emilio Angelina, Gladis Laura Sosa, Nélida M. Peruchena · 2022 · Journal of Chemical Information and Modeling
12. Docking and Scoring in Drug Discovery
    Francesca Spyrakis, Pietro Cozzini, Glen E. Kellogg · 2010 · Burger's Medicinal Chemistry and Drug Discovery
13. Recent computational advances in the identification of cryptic binding sites for drug discovery
    Dorota Gašparíková, Rupesh V. Chikhale, Jason C. Cole, Ehmke Pohl · 2024 · Bioinformatics Advances
14. Diffusion-Based Graph Generative Methods
    Hongyang Chen, Can Xu, Lingyu Zheng, Qiang Zhang, Xuemin Lin · 2024 · IEEE Transactions on Knowledge and Data Engineering
15. TargetSA: adaptive simulated annealing for target-specific drug design
    Zhe Xue, Chenwei Sun, Wenhao Zheng, Jiancheng Lv, Xianggen Liu · 2024 · Bioinformatics
16. Discovering rules for protein-ligand specificity using support vector inductive logic programming
    Lawrence A. Kelley, Paul J. Shrimpton, Stephen Muggleton, Michael J.E. Sternberg · 2009 · Protein Engineering Design and Selection
17. Can docking scoring functions guarantee success in virtual screening?
    Yendrek Velásquez-López, Eduardo Tejera, Yunierkis Pérez‐Castillo · 2022 · Annual reports in medicinal chemistry
18. Incorporating targeted protein structure in deep learning methods for molecule generation in computational drug design
    Lucy Vost, Yael Ziv, Charlotte Mary Deane · 2025 · Chemical Science
19. Dithiocarbamates and dithiocarbonates containing 6-nitrosaccharin scaffold: Synthesis, antimycobacterial activity and in silico target prediction using ensemble docking-based reverse virtual screening
    Muhammed Trawally, Kübra Demir-Yazıcı, Serap İpek Dingiş-Birgül, Kerem Kaya, Atilla Akdemir, Özlen Güzel-Akdemir · 2022 · Journal of Molecular Structure
20. dbHDPLS: A database of human disease-related protein-ligand structures
    Muchun Zhu, Xiaoping Song, Peng Chen, Wenyan Wang, Bing Wang · 2019 · Computational Biology and Chemistry
21. Structure-Based Drug Design with Geometric Deep Learning: A Comprehensive Survey
    Zai-Xin Zhang, Jia-Xian Yan, Yining Huang, Qi Liu, En-Hong Chen, Meng-Di Wang, M. Zitnik · 2025 · ACM Computing Surveys
22. All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds
    Majid Masso · 2017 · BioMed Research International
23. A Strength-Weaknesses-Opportunities-Threats (SWOT) Analysis of Cheminformatics in Natural Product Research
    Benjamin Kirchweger, Judith Maria Rollinger · 2019 · Fortschritte der Chemie Organischer Naturstoffe/Fortschritte der Chemie organischer Naturstoffe/Progress in the chemistry of organic natural products
24. A structural informatics approach to mine kinase knowledge bases
    Natasja Brooijmans, Dominick Mobilio, Gary Walker, Ramaswamy Nilakantan, R. Aldrin Denny, Eric Feyfant, David Diller, Jack Andrew Bikker, Christine C. Humblet · 2009 · Drug Discovery Today
25. DIONYSUS: a database of protein–carbohydrate interfaces
    Aria Gheeraert, T. Bailly, Ya-Ni Ren, Ali Hamraoui, Julie Te, Yann Vander Meersche, Gabriel Cretin, Ravy Leon Foun Lin, Jean-Christophe Gelly, Serge Perez et al. · 2024 · Nucleic Acids Research
26. Flow matching meets biology and life science: a survey
    Zihao Li, Zhichen Zeng, Xiao Lin, Fan Fang, Yanru Qu, Zhe Xu, Zhining Liu, Xuying Ning, Tianxin Wei, Ge Liu et al. · 2026 · npj Artificial Intelligence
27. Mapping drug-target interaction networks
    Longzhang Tian, Shuxing Zhang · 2009 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
28. Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy
    Guo, Binjie, Zheng, Hanyu, Jiang, Haohan, Li, Xiaodan, Guan, Naiyu, Zuo, Yanming, Zhang, Yicheng, Yang, Hengfu, Wang, Xuhua · 2023 · Briefings in Bioinformatics
29. AutoBind: automatic extraction of protein–ligand-binding affinity data from biological literature
    Darby Tien-Hao Chang, Chao-Hsuan Ke, Jung‐Hsin Lin, Jung-Hsien Chiang · 2012 · Bioinformatics
30. Potent inhibition of TGF-βsignaling pathway regulator Abl: potential therapeutics for hepatic fibrosis
    Kuifeng Wang, Yongzhi Tang, Fei Yan, Jiansheng Zhu, Ji‐Cheng Li · 2014 · Journal of Receptors and Signal Transduction
31. Molecular Docking and Virtual Screening to Investigate Lead Compounds for Veterinary Drug Development
    Akansha Agrwal, Neakanshika Chadha, Aman Sahu · 2025 · Springer eBooks
32. Public Domain Databases for Medicinal Chemistry
    George Nicola, Tiqing Liu, Michael K. Gilson · 2013 · Methods and principles in medicinal chemistry
33. A Systematic Review of Drug-Related Interactions─Utilizing Deep Learning and LLMs for Prediction and Mitigation
    Soheila Behrooznia, Mohsen Hooshmand · 2025 · ACS Omega
34. Chirality-Assisted Self-Assembly of Low-Symmetry Noncovalent Capsules with Quantitative Diastereoisomeric Selection
    Grzegorz Markiewicz, Xujun Qiu, Gökay Avcı, Emma Helen Wolpert, Kim E. Jelfs, Jeremy K. M. Sanders, Artur R. Stefankiewicz · 2025 · Journal of the American Chemical Society
35. Drug Repurposing for Thioredoxin Interacting Protein Through Molecular Networking, Pharmacophore Modelling, and Molecular Docking Approaches
    Ayushi Kar, Balamurugan Paramasivam, Darshini Jayakumar, Akey Krishna Swaroop, Jubie Selvaraj · 2023 · Letters in Drug Design & Discovery
36. Novel Macrocyclic Bidentate Schiff’s base Hg (II) Complexes, Hirshfeld surface analysis, NCI analysis, and Antimicrobial activity studies
    Anil Kumar Pal, Amit Jaiswal, Ritu Ravi, Kapil Kumar Yadav, Dharmendra Kumar Sahu, Ranjeet Kumar, Monika Singh · 2024 · Polyhedron
37. Sequence or structure: using bioinformatics and homology modeling to understand functional relationships in cAMP/cGMP binding domains
    Natalie A. LaFranzo, Matthew K. Strulson, Dawn M. Yanker, Luke T. Dang, Joshua A. Maurer · 2010 · Molecular BioSystems
38. ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data
    Emanuel S. R. Ehmki, Torben Gutermuth, Tobias Harren, Stefan Kurtz, Matthias Rarey · 2026 · Journal of Chemical Information and Modeling
39. A Statistical Survey on the Binding Constants of Covalently Bound Protein–Ligand Complexes
    Xun Li, Zhihai Liu, Yan Li, Jie Li, Jiajie Li, Renxiao Wang · 2010 · Molecular Informatics
40. Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology
    2025
41. Docking and Virtual Screening
    Garrett M. Morris · 2012 · Royal Society of Chemistry eBooks
42. Molecular Docking: A Review Paper
    Namrata Arya, Arminder Kaur · 2022 · International Journal of Innovative Research in Engineering & Management
43. Protein-Ligand Binding with Applications in Molecular Docking
    Nikita Mishra, Negin Forouzesh · 2012 · Computational biology
44. Recent Deep Learning Applications to Structure-Based Drug Design
    Jacob C. Verburgt, Anika Jain, Daisuke Kihara · 2023 · Methods in molecular biology
45. SAR Knowledge Bases in Drug Discovery
    Stefan Senger, Andrew R. Leach · 2008 · Annual reports in computational chemistry
46. Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction
    Majid Masso · 2013 · BMC Structural Biology
47. Deep Reinforcement Learning in Healthcare and Biomedical Research
    Shruti Agrawal, Pralay Mitra · 2024 · Wiley eBooks
48. SCORCH2: A Generalized Heterogeneous Consensus Model for High‐Enrichment Interaction‐Based Virtual Screening
    Lin Chen, Vincent Blay, Pedro J. Ballester, Douglas R. Houston · 2025 · Advanced Science
49. Advancements in Large Language Models ( LLMs ): Empowering Drug Discovery
    Bosheng Song, Xiaowen Li, Xiuxiu Chao, Li Sheng Wang, Yiping Liu, Zhen Xia, Dongsheng Cao, Xiangzheng Fu · 2025 · Wiley Interdisciplinary Reviews Computational Molecular Science
50. Global and local integrated gradient-based diffusion model for de novo drug design
    Sejin Park, Minjae Lins Chung, Hyunju Lee · 2026 · Briefings in Bioinformatics
51. Fragment oriented molecular shapes
    Ethan Hain, Carlos Jaime Camacho, David Ryan Koes · 2016 · Journal of Molecular Graphics and Modelling
52. Prediction of kinase-inhibitor binding affinity using energetic parameters
    Usha Singaravelu, Samuel Selvaraj · 2016 · Bioinformation
53. 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
54. Role of Interactions and Volume Variation in Discriminating Active and Inactive Forms of Cyclin‐Dependent Kinase‐2 Inhibitor Complexes
    Saranya Nallusamy, Samuel Selvaraj · 2011 · Chemical Biology & Drug Design
55. Chemoinformatics
    Megan L. Peach, Alexey V. Zakharov, Laura Guasch, Marc C. Nicklaus · 2014 · Elsevier eBooks
56. Small Molecule Docking
    Richard A. Friesner, Matt Repasky, Ramy Farid · 2008 · WORLD SCIENTIFIC eBooks
57. Polypharmacology in Drug Discovery
    Oscar Méndez‐Lucio, J. Jesús Naveja, Hugo Vite‐Caritino, Fernando Daniel Prieto-Martínez, José L. Medina‐Franco · 2017 · Methods and principles in medicinal chemistry
58. Combining Structural, Thermodynamic, and Kinetic Information to Drive Hit‐to‐Lead Progression
    Geoffrey A. Holdgate, Christopher Phillips · 2020
59. Targeting protein-ligand neosurfaces using a generalizable deep learning approach
    Anthony Marchand, Stephen Buckley, Arne Schneuing, Martin Pačesa, Pablo Gaínza, Evgenia Elizarova, Rebecca M. Neeser, Pao‐Wan Lee, Luc Reymond, Maddalena Elia et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
60. Molecular embedding-based algorithm selection in protein-ligand docking
    Jiabao Brad Wang, Siyuan Cao, Hongxuan Wu, Yiliang Yuan, Mustafa Mısır · 2026 · Journal of Cheminformatics
61. Unified protein–small molecule graph neural networks for binding site prediction
    Jian Wang, Nikolay V. Dokholyan · 2026 · Proceedings of the National Academy of Sciences
62. Unraveling the diversity of protein-carbohydrate interfaces: Insights from a multi-scale study
    Aria Gheeraert, Frédéric Guyon, Serge Pérez, Tatiana V. Galochkina · 2025 · Carbohydrate Research
63. Impact of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking of protein–ligand complexes
    Saranya Nallusamy, Jeyaraman Jeyakanthan, S. Selvaraj · 2012 · Bioorganic & Medicinal Chemistry Letters
64. Testing the sensitivities of noncognate inhibitors to varicella zoster virus thymidine kinase: implications for postherpetic neuralgia therapy with existing agents
    Lianjuan Yang, Xiaohui Mo, Hong Jun Yang, Hejun Dai, Fei Tan · 2014 · Journal of Molecular Modeling
65. MLDB: macromolecule ligand database
    S. E. Saravanan, R. Karthi, K. Sathish, K. Kokila, Radhakrishnan Sabarinathan, K. Sekar · 2009 · Journal of Applied Crystallography
66. UPDATING BINDING MOAD — DATA MANAGEMENT AND INFORMATION WORKFLOW
    Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Heather A. Carlson, BRANDON DIMCHEFF, PETER DRESSLAR · 2010 · New Mathematics and Natural Computation
67. Knowledge-based scoring function derived from atomic tessellation of macromolecular structures for prediction of protein-ligand binding affinity
    Majid Masso · 2012 · IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
68. Computational Structure–Activity Relationship Studies of Epigenetic Target Inhibitors
    Oscar Méndez‐Lucio · 2016 · Elsevier eBooks
69. A Multibody Atomic Statistical Potential for Predicting Enzyme-Inhibitor Binding Energy
    Majid Masso · 2013 · Biophysical Journal
70. Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein‐ligand Complexes
    Raed Khashan, Alexander Tropsha, Weifan Zheng · 2022 · Molecular Informatics
71. Protein-ligand binding sites. Identification, characterization and interrelations
    Peter Schmidtke · 2011 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
72. High throughput screening with machine learning
    Oleksandr Gurbych, Maksym Druchok, Dzvenymyra Yarish, Sofiya Garkot · 2020 · arXiv (Cornell University)
73. More Accurate Binding Affinity Prediction Using Protein Homology and Ligand-Based Transfer Learning
    Justin Clement Purnomo, Caitlin Kim, Kunyang Sun, Yingze Wang, Teresa L. Head-Gordon · 2026 · Journal of Chemical Information and Modeling
74. How and Why Does Knowledge‐Based Biased Docking Improve Molecular Docking Performance?
    Juan Manuel Prieto, Jorge Octavio Lannot, Camila Mara Clemente, Carlos Pablo Modenutti, Adrian Gustavo Turjanski, Marcelo Adrian Marti · 2026 · ChemMedChem
75. Using generative AI to transform peptide hits into small molecule leads
    Joshua Mills, Yu Heng Lau · 2026 · Beilstein Journal of Organic Chemistry
76. Comparison of non-sequential sets of protein residues
    Leonardo D. Garma, André H. Juffer · 2015 · Computational Biology and Chemistry
77. 药物研发领域中的开放访问数据库
    Zhihai Liu, Jie Li, Wei Nie, Renxiao Wang, Yan Li, Li Han, Yuchen Liu, Jie Liu · 2015 · Scientia Sinica Chimica
78. <scp>DisDock</scp> : A Deep Learning Method for Metal Ion‐Protein Redocking
    Lin, Menghan, Li, Keqiao, Zhang, Yuan, Pan, Feng, Wu, Wei, Zhang, Jinfeng · 2025 · Proteins: Structure, Function, and Bioinformatics
79. Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors
    Francesca Spyrakis, Pietro Cozzini, Glen E. Kellogg · 2016 · Nuclear Receptor Research
80. A multibody atomic statistical potential for the prediction of enzyme-inhibitor binding energy
    Majid Masso · 2012 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
81. Receptor–Ligand Interactions in Biological Systems
    Liwei Li, Samy O. Meroueh · 2008 · Wiley Encyclopedia of Chemical Biology
82. GlycoTorch Vina: Improved Docking of Sulfated Sugars Using QM-derived Scoring Functions
    Eric D. Boittier, Jed M. Burns, Neha S. Gandhi, Vito Ferro · 2020 · ChemRxiv
83. Protein-Ligand Binding Site Prediction and De Novo Ligand Generation from Cryo-EM Maps
    Chunyang Lu, Kaustav Mitra, Kiran Mitra, Hanze Meng, Shane T. Rich-New, Fengbin Wang, Dong Si · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
84. SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design
    Peidong Zhang, Rong Han, Xiangzhe Kong, Ting Chen, Jianzhu Ma · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
85. Bridging Chemical and Biological Information: Public Knowledge Spaces
    Paul A Thiessen, Wolf‐D. Ihlenfeldt, Evan Bolton, Stephen H. Bryant · 2011
86. Protein structure prediction and structure -based protein function annotation
    Ambrish Roy · 2011 · KU ScholarWorks (The University of Kansas)
87. Computational Design of Small Molecule Binding Proteins
    Austin L. Day · 2015 · ResearchWorks at the University of Washington (University of Washington)
88. EDUCATIONAL AND PROFESSIONAL EXPERIENCE
    Irta Postdoctoral Fellow, Richard W. Pastor, Warren L. DeLano, Ricoh Silicon Valley · 2011
89. Metabólitos secundários como potenciais inibidores de CDK8 (proteína quinase humana)
    Buana Carvalho de Almeida · 2018
90. Structural Investigation of Binding Events in Proteins
    Jordan J. Clark · 2018 · Deep Blue (University of Michigan)
91. 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
92. Inhibition of Quorum Sensing Regulated Protein of E. coli using Food-based Biomolecules
    Kothandapani Sundar, S Melinger Joseph, K. Kumara Guru, G. Jayalakshmi · 2022 · Asian Journal of Biological Sciences
93. Discovery of Novel Metalloenzyme Inhibitors Based on Property Characterization: Strategy and Application for HDAC1 Inhibitors
    Lu Zhang, Yajun Yang, Ying Yang, Zhiyan Xiao · 2024 · Molecules
94. Unified Guidance for Geometry-Conditioned Molecular Generation
    Sirine Ayadi, Leon Hetzel, Johanna Sommer, Fabian Joachim Theis, Stephan Günnemann · 2025 · Qeios
95. Molecular Docking: A Gateway to Rational Drug Design and Precision Medicine
    ShirsathPriya .K ShirsathPriya .K, AhirraoSangita .A AhirraoSangita .A, Wankhede Neha. B Wankhede Neha. B, Suryawanshi Shraddha.N *Suryawanshi Shraddha.N, Prof.MairalPooja.B Prof.MairalPooja.B, Tufail Dana Tufail Dana, *Prof. Nikam .M.B *Prof. Nikam .M.B · 2025 · International Journal of Pharmaceutical Research and Applications
96. Allo-DiffHopping: A Computational Approach for Allosteric Scaffold Hopping Using Conditional E(3) Equivariant Diffusion Models
    Victor Li, Yu Sun · 2024 · International Conference on Computational Biology and Bioinformatics (ICCBB)
97. Generative models for drug design
    Yijin Zhou, Y. Wang · 2025 · Elsevier eBooks
98. Evolutionary and geometric signatures reveal ligand-binding sites across proteomes
    Stelina Tarasi, Laura Malo, Alexis Molina · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
99. A Primer on SAnDReS 2.0 for Scoring Function Design
    Amauri Duarte da Silva, Martina Veit‐Acosta, Olga A. Tarasova, Walter Filgueira de Azevedo · 2025 · Methods in molecular biology
100. Molegro Data Modeller for Machine Learning
     Amauri Duarte da Silva, Nelson José Freitas da Silveira, Patrícia Rufino Oliveira, Walter Filgueira de Azevedo · 2025 · Methods in molecular biology