AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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2. Biodegradation of poly(ethylene terephthalate): Mechanistic insights, advances, and future innovative strategies
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3. Nickel(II)-Schiff base complex recognizing domain II of bovine and human serum albumin: Spectroscopic and docking studies
   Aurkie Ray, Banabithi Koley Seth, Uttam Pal, Samita Basu · 2012 · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy
4. Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3
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5. Design, synthesis and anti-Alzheimer’s activity of novel 1,2,3-triazole-chromenone carboxamide derivatives
   Arezoo Rastegari, Hamid Nadri, Mohammad Reza Mahdavi, Alireza Moradi, Seyedeh Sara Mirfazli, Najmeh Edraki, Farshad Homayouni Moghadam, Bagher A. Larijani, Tahmineh Akbarzadeh, Mina Saeedi · 2018 · Bioorganic Chemistry
6. Plant-derived antiviral drugs as novel hepatitis B virus inhibitors: Cell culture and molecular docking study
   Mohammad Khalid Parvez, Md Tabish Rehman, Perwez Alam, Mohammed Salem Al-Dosari, Saleh Ibrahim Alqasoumi, Mohamed Fahad Alajmi · 2018 · Saudi Pharmaceutical Journal
7. Novel Computational Approach to Predict Off-Target Interactions for Small Molecules
   Mohan S. Rao, Rishi Gupta, Michael J. Liguori, Mufeng Hu, Xin Huang, Srinivasa Raju Mantena, Scott W. Mittelstadt, Eric A.G. Blomme, Terry R. Van Vleet · 2019 · Frontiers in Big Data
8. COSY catalyses trans–cis isomerization and lactonization in the biosynthesis of coumarins
   Ruben Vanholme, Lisa Sundin, Keletso Carol Seetso, Hoon Kim, Xinyu Liu, Jin Li, Barbara De Meester, Lennart Hoengenaert, Geert Goeminne, Kris Morreel et al. · 2019 · Nature Plants
9. Diffusion Models in De Novo Drug Design
   Amira A. Alakhdar, Barnabás Póczos, Newell R. Washburn · 2024 · Journal of Chemical Information and Modeling
10. Engineering a de Novo Transport Tunnel
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11. Mechanism of quercetin therapeutic targets for Alzheimer disease and type 2 diabetes mellitus
    Guoxiu Zu, Keyun Sun, Ling Li, Xiuli Zu, Tao Han, Hailiang Huang · 2021 · Scientific Reports
12. Imaging α-synuclein pathologies in animal models and patients with Parkinson’s and related diseases
    Hironobu Endo, Maiko Ono, Yuhei Takado, Kiwamu Matsuoka, Manami Takahashi, Kenji Tagai, Yuko Kataoka, Kosei Hirata, Keisuke Takahata, Chie Seki et al. · 2024 · Neuron
13. Caffeine Inhibits Acetylcholinesterase, But Not Butyrylcholinesterase
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14. Synthesis and anticancer activity of novel water soluble benzimidazole carbamates
    Jae Eun Cheong, Michela Zaffagni, Ivy Chung, Yingjie Xu, Yiqiang Wang, Finith E. Jernigan, Bruce R. Zetter, Lijun Sun · 2017 · European Journal of Medicinal Chemistry
15. Acoplamiento Molecular: Avances Recientes y Retos
    Fernando Daniel Prieto-Martínez, Marcelino Arciniega, José L. Medina‐Franco · 2018 · TIP Revista Especializada en Ciencias Químico-Biológicas
16. Haloperidol bound D2 dopamine receptor structure inspired the discovery of subtype selective ligands
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17. Molecular Investigation of SARS–CoV-2 Proteins and Their Interactions with Antiviral Drugs
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18. In silico molecular docking in DNA aptamer development
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19. Network pharmacology-based investigation of potential targets of astragalus membranaceous-angelica sinensis compound acting on diabetic nephropathy
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20. Synthesis and evaluation of 4-substituted coumarins as novel acetylcholinesterase inhibitors
    Seyyede Faeze Razavi, Mehdi Khoobi, Hamid Nadri, Amirhossein Sakhteman, Alireza Moradi, Saeed Emami, Alireza Foroumadi, Abbas Shafiee · 2013 · European Journal of Medicinal Chemistry
21. Anticolon Cancer Activity of Largazole, a Marine-Derived Tunable Histone Deacetylase Inhibitor
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22. Abscisic Acid Regulates Inflammation via Ligand-binding Domain-independent Activation of Peroxisome Proliferator-activated Receptor γ
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23. A new piperidinol derivative targeting mycolic acid transport in Mycobacterium abscessus
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24. Discovery of Nanomolar Dengue and West Nile Virus Protease Inhibitors Containing a 4-Benzyloxyphenylglycine Residue
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25. Predicting complexation performance between cyclodextrins and guest molecules by integrated machine learning and molecular modeling techniques
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26. Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies
    Abdallah S. Abdelsattar, Alyaa Dawoud, Mohamed A. Helal · 2020 · Nanotoxicology
27. Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
    Germano Heinzelmann, Michael K. Gilson · 2021 · Scientific Reports
28. Inactivation of lipoxygenase and cyclooxygenase by natural betalains and semi-synthetic analogues
    Pedro J. Vidal, Manuel López-Nicolás, Fernando Gandía‐Herrero, Francisco García‐Carmona · 2014 · Food Chemistry
29. Protein Kinase CK-1 Inhibitors As New Potential Drugs for Amyotrophic Lateral Sclerosis
    Irene G. Salado, Miriam Redondo, Murilo Lamim Bello, Concepción Pérez, Nicole F. Liachko, Brian C. Kraemer, Laëtitia Miguel, Magalie Lecourtois, Carmen Gil, Ana Martı́nez et al. · 2014 · Journal of Medicinal Chemistry
30. Multiple Transport-Active Binding Sites Are Available for a Single Substrate on Human P-Glycoprotein (ABCB1)
    Eduardo E. Chufán, Khyati Kapoor, Hong May Sim, Satyakam Singh, Tanaji T. Talele, Stewart R. Durell, Suresh V. Ambudkar · 2013 · PLoS ONE
31. The glucosinolate breakdown product indole‐3‐carbinol acts as an auxin antagonist in roots of <i><scp>A</scp>rabidopsis thaliana</i>
    Katz, Ella, Nisani, Sophia, Yadav, Brijesh S., Woldemariam, Melkamu G., Shai, Ben, Obolski, Uri, Ehrlich, Marcelo, Shani, Eilon, Jander, Georg, Chamovitz, Daniel A. · 2015 · The Plant Journal
32. Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis
    Kinya Hotta, Xi Chen, Robert S. Paton, Atsushi Minami, Hao Li, Kunchithapadam Swaminathan, Irimpan I. Mathews, Kenji Watanabe, Hideaki Oikawa, Kendall N. Houk et al. · 2012 · Nature
33. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance
    Jody Emile Phelan, Francesc Coll, Ruth McNerney, David Benjamin Ascher, Douglas E. V. Pires, Nicholas Furnham, Nele Coeck, Grant A. Hill-Cawthorne, Mridul B. Nair, Kim Mallard et al. · 2016 · BMC Medicine
34. SLC2A8 (GLUT8) is a mammalian trehalose transporter required for trehalose-induced autophagy
    Allyson L. Mayer, Cassandra B. Higgins, Monique R. Heitmeier, Thomas E. Kraft, Xia Qian, Jan R. Crowley, Krzysztof L. Hyrc, Wandy L. Beatty, Kevin E. Yarasheski, Paul W. Hruz et al. · 2016 · Scientific Reports
35. SPA70 is a potent antagonist of human pregnane X receptor
    Wenwei Lin, Yueming Wang, Sergio C. Chai, Lili Lv, Jie Zheng, Jing Wu, Qijun Zhang, Yong‐Dong Wang, Patrick R. Griffin, Taosheng Chen · 2017 · Nature Communications
36. RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks
    Hussein Hassan Harrirou, Ce Zhang, Thomas Lemmin · 2020 · Journal of Chemical Information and Modeling
37. Structural bioinformatics-based protein engineering of thermo-stable PETase from Ideonella sakaiensis
    Hyeoncheol Francis Son, Seongjoon Joo, Hogyun Seo, Hye-Young Sagong, Seul Hoo Lee, Hwaseok Hong, Kyung‐Jin Kim · 2020 · Enzyme and Microbial Technology
38. Dissection of the general two-step di- C -glycosylation pathway for the biosynthesis of (iso)schaftosides in higher plants
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39. Inhibition of the SARS-CoV-2 3CLpro main protease by plant polyphenols
    Miha Bahun, Marko Jukič, Domen Oblak, Luka Kranjc, Gregor Bajc, Matej Butala, Krištof Bozovičar, Tomaž Bratkovič, Črtomir Podlipnik, Nataša Poklar Ulrih · 2021 · Food Chemistry
40. Robust enzyme discovery and engineering with deep learning using CataPro
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41. In silico and in vitro evaluation of kaempferol as a potential inhibitor of the SARS‐CoV ‐2 main protease ( 3CLpro )
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42. Predictiveness curves in virtual screening
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43. Heparan sulfate proteoglycans present PCSK9 to the LDL receptor
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44. Investigation of molecular mechanism of recognition between citral and MARK4: A newer therapeutic approach to attenuate cancer cell progression
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45. Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches
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46. In vitro and in silico anti-dengue activity of compounds obtained from Psidium guajava through bioprospecting
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47. Synthesis, structural, molecular docking and spectroscopic studies of (E)-N'-(4-methoxybenzylidene)-5-methyl-1H-pyrazole-3-carbohydrazide
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48. Molecular docking and ADMET study of bioactive compounds of Glycyrrhiza glabra against main protease of SARS-CoV2
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49. OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells
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50. Molecular docking-based computational platform for high-throughput virtual screening
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51. Novel coumarin derivatives bearing N-benzyl pyridinium moiety: Potent and dual binding site acetylcholinesterase inhibitors
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52. Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators
    Reed B. Jacob, Tim Andersen, Owen M. McDougal · 2012 · PLoS Computational Biology
53. SAnDReS a Computational Tool for Statistical Analysis of Docking Results and Development of Scoring Functions
    Mariana Morrone Xavier, Gabriela Sehnem Heck, Maurício Boff de Ávila, Nayara Maria Bernhardt Levin, Val Oliveira Pintro, Nathalia Lemes Carvalho, Walter Filgueira de Azevedo · 2016 · Combinatorial Chemistry & High Throughput Screening
54. Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery
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55. Identification of FDA-Approved Drugs as Antivirulence Agents Targeting the pqs Quorum-Sensing System of Pseudomonas aeruginosa
    Francesca D’Angelo, Valerio Baldelli, Nigel Halliday, Paolo Pantalone, Fabio Polticelli, Ersilia Vita Fiscarelli, Paul M. Williams, Paolo Visca, Livia Leoni, Giordano Rampioni · 2018 · Antimicrobial Agents and Chemotherapy
56. Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions
    Jianing Lu, Xuben Hou, Cheng Wang, Yingkai Zhang · 2019 · Journal of Chemical Information and Modeling
57. Identification of potential inhibitors of SARS-CoV-2 main protease from Aloe vera compounds: A molecular docking study
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58. Docking-Based Virtual Screening Using PyRx Tool: Autophagy Target Vps34 as a Case Study
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59. Separation, identification, and molecular docking of tyrosinase inhibitory peptides from the hydrolysates of defatted walnut (Juglans regia L.) meal
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60. Exploring the Molecular Mechanism of Action of Yinchen Wuling Powder for the Treatment of Hyperlipidemia, Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation
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61. The structure of SpnF, a standalone enzyme that catalyzes [4 + 2] cycloaddition
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62. Mechanistic Insights into Xenon Inhibition of NMDA Receptors from MD Simulations
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63. Novel coumarin-3-carboxamides bearing N-benzylpiperidine moiety as potent acetylcholinesterase inhibitors
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64. Molecular Docking in Formulation and Development
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66. A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem)
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67. Lycorine, a non-nucleoside RNA dependent RNA polymerase inhibitor, as potential treatment for emerging coronavirus infections
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68. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor
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73. Functional architecture of MFS d -glucose transporters
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74. Development of 3,5-Dinitrobenzylsulfanyl-1,3,4-oxadiazoles and Thiadiazoles as Selective Antitubercular Agents Active Against Replicating and Nonreplicating Mycobacterium tuberculosis
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75. Predicting P-Glycoprotein-Mediated Drug Transport Based On Support Vector Machine and Three-Dimensional Crystal Structure of P-glycoprotein
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84. Novel tacrine-1,2,3-triazole hybrids: In vitro, in vivo biological evaluation and docking study of cholinesterase inhibitors
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90. Is oseltamivir suitable for fighting against COVID-19: In silico assessment, in vitro and retrospective study
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95. Physico-chemical characterization of carvacrol loaded zein nanoparticles for enhanced anticancer activity and investigation of molecular interactions between them by molecular docking
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98. The binding selectivity of vonoprazan ( TAK ‐438) to the gastric H + ,K + ‐ ATP ase
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100. Bioactive peptide with antioxidant and anticancer activities from black soybean [Glycine max (L.) Merr.] byproduct: isolation, identification and molecular docking study
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