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

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3. Molecular Docking and Virtual Screening Based Prediction of Drugs for COVID-19
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6. Multidimensional in silico strategy for identification of natural polyphenols-based SARS-CoV-2 main protease (Mpro) inhibitors to unveil a hope against COVID-19
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7. The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease
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8. Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method
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9. Synthesis and anticholinesterase activity of coumarin-3-carboxamides bearing tryptamine moiety
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11. Structural modeling of HLA-B*1502/peptide/carbamazepine/T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis
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12. Structural Insights into SraP-Mediated Staphylococcus aureus Adhesion to Host Cells
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13. Thiamine and selected thiamine antivitamins — biological activity and methods of synthesis
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14. Complexation of trans- and cis-resveratrol with bovine serum albumin, β-lactoglobulin or α-lactalbumin
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15. Synergistic Effects of Curcumin and Piperine as Potent Acetylcholine and Amyloidogenic Inhibitors With Significant Neuroprotective Activity in SH-SY5Y Cells via Computational Molecular Modeling and in vitro Assay
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16. The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model
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17. Clinically Approved Drugs Inhibit the Staphylococcus aureus Multidrug NorA Efflux Pump and Reduce Biofilm Formation
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18. Hypoxia-induced GBE1 expression promotes tumor progression through metabolic reprogramming in lung adenocarcinoma
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19. Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach
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20. Network pharmacology for the identification of phytochemicals in traditional Chinese medicine for COVID-19 that may regulate interleukin-6
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21. Development of isatin-thiazolo[3,2-a]benzimidazole hybrids as novel CDK2 inhibitors with potent in vitro apoptotic anti-proliferative activity: Synthesis, biological and molecular dynamics investigations
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22. Yin-xing-tong-mai decoction attenuates atherosclerosis via activating PPARγ-LXRα-ABCA1/ABCG1 pathway
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23. Pathogenesis of IgA Nephropathy: Current Understanding and Implications for Development of Disease-Specific Treatment
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24. Hot spots-making directed evolution easier
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25. Natural Variants of the KPC-2 Carbapenemase have Evolved Increased Catalytic Efficiency for Ceftazidime Hydrolysis at the Cost of Enzyme Stability
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26. Imaging Therapeutic PARP Inhibition In Vivo through Bioorthogonally Developed Companion Imaging Agents
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27. Development of the next generation of HIV-1 integrase inhibitors: Pyrazolone as a novel inhibitor scaffold
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28. Delayed Treatment With 4-Methylpyrazole Protects Against Acetaminophen Hepatotoxicity in Mice by Inhibition of c-Jun n-Terminal Kinase
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29. In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules
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30. PAMAM Dendrimer–Drug Interactions: Effect of pH on the Binding and Release Pattern
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31. Computational tools for enzyme improvement: why everyone can – and should – use them
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32. Long-term protein packaging in cholinium-based ionic liquids: improved catalytic activity and enhanced stability of cytochrome c against multiple stresses
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33. Tackling neuroinflammation and cholinergic deficit in Alzheimer's disease: Multi-target inhibitors of cholinesterases, cyclooxygenase-2 and 15-lipoxygenase
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34. Learning from the ligand: using ligand-based features to improve binding affinity prediction
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35. Computational design of enzymes for biotechnological applications
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36. Experimental, molecular docking and molecular dynamic studies of natural products targeting overexpressed receptors in breast cancer
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37. Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening
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38. A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes
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39. Grassystatins A−C from Marine Cyanobacteria, Potent Cathepsin E Inhibitors That Reduce Antigen Presentation
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40. Design, synthesis, biological evaluation and docking study of 5-oxo-4,5-dihydropyrano[3,2-c]chromene derivatives as acetylcholinesterase and butyrylcholinesterase inhibitors
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41. Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication
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42. Glutathione regulates ACC synthase transcription via WRKY33 and ACC oxidase by modulating mRNA stability to induce ethylene synthesis during stress
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43. Computer-Assisted Drug Formulation Design: Novel Approach in Drug Delivery
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44. Structures of PPARγ complexed with lobeglitazone and pioglitazone reveal key determinants for the recognition of antidiabetic drugs
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45. Synthesis and spectroscopic study of three new oxadiazole derivatives with detailed computational evaluation of their reactivity and pharmaceutical potential
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46. The fungal ligand chitin directly binds TLR2 and triggers inflammation dependent on oligomer size
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47. Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of some in-house molecules as papain-like protease (PLpro) inhibitors
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48. Network pharmacology, molecular docking integrated surface plasmon resonance technology reveals the mechanism of Toujie Quwen Granules against coronavirus disease 2019 pneumonia
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49. A molecular docking and molecular dynamics simulation study on the interaction between cyanidin ‐ 3 ‐O ‐glucoside and major proteins in cow's milk
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50. Conversion of RNA Aptamer into Modified DNA Aptamers Provides for Prolonged Stability and Enhanced Antitumor Activity
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51. 1,2,3-Triazoles of 8-Hydroxyquinoline and HBT: Synthesis and Studies (DNA Binding, Antimicrobial, Molecular Docking, ADME, and DFT)
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52. ExploringKlebsiella pneumoniaecapsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia
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53. Design and Prediction of Aptamers Assisted by In Silico Methods
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54. Tylophorine, a phenanthraindolizidine alkaloid isolated from Tylophora indica exerts antiangiogenic and antitumor activity by targeting vascular endothelial growth factor receptor 2–mediated angiogenesis
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55. β-Glucuronidases of opportunistic bacteria are the major contributors to xenobiotic-induced toxicity in the gut
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56. Directed evolution of RebH for catalyst-controlled halogenation of indole C–H bonds
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57. α-Glucosidase inhibitory effect of anthocyanins from Cinnamomum camphora fruit: Inhibition kinetics and mechanistic insights through in vitro and in silico studies
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58. Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition
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60. In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents
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61. Antidiabetic Food-Derived Peptides for Functional Feeding: Production, Functionality and In Vivo Evidences
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62. Synthesis, crystal structure, vibrational spectral investigation, intermolecular interactions, chemical reactivity, NLO properties and molecular docking analysis on (E)-N-(4-nitrobenzylidene)-3-chlorobenzenamine: A combined experimental and theoretical study
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63. A facile approach synthesis of benzoylaryl benzimidazole as potential α-amylase and α-glucosidase inhibitor with antioxidant activity
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64. BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction
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65. CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an l-proline exporter for l-proline hyperproduction
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66. Synthesis, molecular docking and DFT analysis of novel bis-Schiff base derivatives with thiobarbituric acid for α-glucosidase inhibition assessment
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67. Machine learning consensus scoring improves performance across targets in structure-based virtual screening.
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68. Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction
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69. Rhodamine–Hoechst positional isomers for highly efficient staining of heterochromatin
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70. Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle
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71. Computational investigation on Andrographis paniculata phytochemicals to evaluate their potency against SARS-CoV-2 in comparison to known antiviral compounds in drug trials
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72. Structural insight into the role of novel SARS-CoV-2 E protein: A potential target for vaccine development and other therapeutic strategies
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73. Assessment of antiviral potencies of cannabinoids against SARS-CoV-2 using computational and in vitro approaches
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74. Polyphenols Weaken Pea Protein Gel by Formation of Large Aggregates with Diminished Noncovalent Interactions
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75. Generating property-matched decoy molecules using deep learning
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77. Engineering an efficient and enantioselective enzyme for the Morita–Baylis–Hillman reaction
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79. Emerging Methods for Ensemble-Based Virtual Screening
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81. Potent selective monoamine oxidase B inhibition by maackiain, a pterocarpan from the roots of Sophora flavescens
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82. Structure-Based Virtual Screening
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83. Altered physiochemical properties in industrially synthesized ZnO nanoparticles regulate oxidative stress; induce in vivo cytotoxicity in embryonic zebrafish by apoptosis
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84. Molecular docking, Hirshfeld surface, structural, spectroscopic, electronic, NLO and thermodynamic analyses on novel hybrid compounds containing pyrazole and coumarin cores
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85. Bioaccumulation in the gut and liver causes gut barrier dysfunction and hepatic metabolism disorder in mice after exposure to low doses of OBS
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86. DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity
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88. Structural-based virtual screening and identification of novel potent antimicrobial compounds against YsxC of Staphylococcus aureus
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89. An accurate and universal protein-small molecule batch docking solution using Autodock Vina
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90. A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila
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91. Novel N-substituted indole Schiff bases as dual inhibitors of cyclooxygenase-2 and 5-lipoxygenase enzymes: Synthesis, biological activities in vitro and docking study
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95. Nanoparticle-Encapsulated Curcumin Inhibits Diabetic Neuropathic Pain Involving the P2Y12 Receptor in the Dorsal Root Ganglia
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96. Mixed-ligand Cu(II) hydrazone complexes designed to enhance anticancer activity
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97. Ligand-based design identifies a potent NUPR1 inhibitor exerting anticancer activity via necroptosis
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98. Phenolic compounds from coffee by-products modulate adipogenesis-related inflammation, mitochondrial dysfunction, and insulin resistance in adipocytes, via insulin/PI3K/AKT signaling pathways
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99. Combined spectroscopic and molecular docking study on the pH dependence of molecular interactions between β-lactoglobulin and ferulic acid
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