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131 results for “Molecular Docking”
Dataset of molecular docking data of neuropeptides to acid-sensing ion channels
<p>The *.dock4 files are result files of molecular docking with the software Autodock Vina to the human ASIC1a closed state model, of the peptides FRRFa and KNFLRFa (FRRF.dock4, KNFLRF.dock4) that can be visualized with structure viewing programs such as UCSF Chimera on the closed ASIC1a model file (closed_ASIC_pH7.4.pdb). The file “FRRF_KNFLRF_complexes.pdb” provides the structures of selected poses of FRRFa and KNFLRFa peptides docked to the closed conformation of the human ASIC1a model.</p>
Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids
<p>This is the "parent" repository for the Data Note : "­Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli.</p> <p>It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it.</p> <p>It also contains a shell script (<strong>create_sim4_repeats.sh</strong>) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one.</p> <p>Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study.</p> <p>Description of files in this dataset:</p> <p><strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10.</p> <p><strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2.</p> <p>Details of how this data was produced is available in the Abelak_etal_Methods.docx document.</p>
Benchmark Data for Attracting Cavities 2.0 Small-Molecular Docking Program
<p>This repository provides data from the following article:<br> <br> U.F. Roehrig, M. Goullieux, M. Bugnon, V. Zoete,<br> Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking.<br> J. Chem. Inf. Modeling 2023<br> https://doi.org/10.1021/acs.jcim.3c00054<br> <br> </p>
Molecular docking: Hydroxychloroquine alternative to inhibit the COVID-19 main protease (MPro)
<p>Docking study shows best binding affinity against the main protease of COVID-19. As per the docking results top twelve compounds as a MPro inhibitor, Coumermycin A1 (-10.2), Irinotecan (-9.4), Suramin (-9.4), Trovafloxacin (-9.3), Aclarubicin (-9.0), Dactinomycin (-9.0), TG-100801 (-9.0), Raltegravir (-8.9), Digoxin (-8.9), Etoposide (-8.9), Doxorubicin (-8.8), and Venetoclax (-8.8) from the tested compounds.</p> <p>ARULANANDAM, CHARLI DEEPAK (2020): Molecular docking: Hydroxychloroquine alternative to inhibit the COVID-19 main protease (MPro). figshare. Dataset. https://doi.org/10.6084/m9.figshare.12032745.v26</p>
AA-Score: a New Scoring Function Based on Amino Acid Specific Interaction for Molecular Docking
<p>The protein-ligand scoring function plays an important role in computer-aided drug discovery, which is heavily used in virtual screening and lead optimization. In this study, we developed a new empirical protein-ligand scoring function, which is a linear combination of empirical energy components, including hydrogen bond, van der Waals, electrostatic, hydrophobic, π-stacking, π-cation, and metal-ligand interaction. Different from previous empirical scoring functions, AA-Score uses several amino acid-specific empirical interaction components. We tested AA-Score on several test sets. The resulting performance shows AA-Score performs well on scoring, docking, and ranking compared with other widely used traditional scoring functions. Our results suggest that AA-Score gains substantial improvements from using detailed protein-ligand interaction components. Besides, we developed an easy-to-use tool to analyze protein-ligand interaction fingerprint and predict binding affinity using AA-Score.</p>
Figure 8 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 8. Representation of complex isosurface (A, C, and E) and 2D interactions within the enzyme active site (B, D, and F): AG/5TIQ (A, B); AE/5TIQ (C, D); PU/5TIQ (E, F).
Figure 7 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 7. Representation of complex ribbons (A, C, and E) and 2D interactions within the enzyme active site (B, D, and F): AG/5TIQ (A, B); AE/5TIQ (C, D); PU/5TIQ (E, F).
Figure 4 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 4. Spectra of 1H-NMR (A) and J-resolved 1H-1H (B) expanded on the region of aromatic signals of the acetanolic subfraction - washing water - acids (88.82%) of L. pacari obtained in methanol-d4.
Figure 3 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 3. (A) Scores of PCA (71.5% PC1 and 21.3% PC2) of 6 subfractions obtained from the ethanolic extract of L. pacari classified by (RT%) activity of each subfraction. (B) Loadings from PC1 (71.5%) with NMR signals discriminating between subfractions.
Figure 5. Spectrum region HSQC 1H-13C in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 5. Spectrum region HSQC 1H-13C (A) and HMBC 1H-13C (B) with region of aromatics compounds of the acid wash water acetate subfraction (88.83%) of L. pacari obtained in methanol-d4.
Figure 2 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 2. Scores of PCA of obtained subfractions from the ethanolic extract of L.pacari classified by the (RT%) activity of each subfraction.
Figure 1 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 1. Profile of 1H-NMR spectra of subfractions obtained from the ethanolic extract of L. pacari classified by (RT%) activity of each subfraction.
Figure 2 in Assessment of melatonin-alpha adrenergic receptor complexes by molecular docking analysis
Figure 2. Two-dimensional schematic diagrams of the intermolecular interactions in the complexes between ligand melatonin and alpha-2A adrenergic receptor 6kux (A) and 6kuy (B). The ligand melatonin is positioned in the center of the diagrams and its nitrogen, oxygen and carbon atoms are indicated in blue, red and black spheres, respectively, connected to each other by solid blue lines. The amino acids Asp113 and Ser204 of the active binding sites of the receptor proteins are indicated by nitrogen, oxygen and carbon atoms represented as blue, red and black spheres, respectively, connected to each other by solid yellow lines. Hydrogen bonding interactions in the ligand-receptor complexes are represented in green dashed lines with their respective distances in angstroms Å. Hydrophobic contacts are represented in red arcs with spokes radiating towards the ligand atoms they contact, and the contacted atoms are shown with spokes radiating back.
Figure 1 in Assessment of melatonin-alpha adrenergic receptor complexes by molecular docking analysis
Figure 1. Molecular docking interactions of the ligand melatonin (in green) in the active binding sites of the adrenoceptors visualized from UCSF Chimera1.15. Tridimensional structures of the adrenergic receptors 6kux in purple (A) and 6kuy in pink (B).
An exploration of human γD-crystallin affinity for potential aggregation inhibitors: A molecular docking investigation
<p><span>These files contain the supplementary material to the article “An exploration of human γD-crystallin affinity for potential aggregation inhibitors: A molecular docking investigation” and the molecular docking simulation data.</span></p> <p><span>In this study, we performed a comparative molecular docking analysis of several experimentally investigated molecules of natural origin, that might protect γ-crystallins from destabilization and aggregation. Our specific protein targets are wild-type human γD-crystallin, and its mutant P23T γD-crystallin, associated with congenital cataract. Thirteen phytochemicals were investigated as potential inhibitors of γD-crystallin aggregation, and we compared their binding energies with those of lanosterol, an ingredient present in over-the-counter eye products, to prevent cataracts. We performed a detailed comparative molecular docking analysis and we found that the binding energies of lanosterol outcompete those of all the other investigated potential natural inhibitors.</span></p>
Molecular docking COVID-19
<p>Coronavirus disease 2019 drug discovery through molecular docking</p>
Table of Molecular Docking Result
<p>Tabulation of Molecular Docking Result for Journal Article: <strong>COMPUTATIONAL EXAMINATION </strong><strong>OF FLAVONOID COMPOUNDS: UTILIZATION OF MOLECULAR SIMULATION TO DISCOVER DRUG CANDIDATE FOR COVID-19</strong></p>
Interaction of Surface Glycoprotein of SARS-CoV-2 Variants of Concern with Potential Drug Candidates: A Molecular Docking Study
<p>This dataset contains additional docking images of SARS-CoV-2 Variants of Concern with drugs under study. It also contains a spreadsheet containing binding residues with different types of bonds. Further it includes the raw spike protein sequences, 3D model of spike proteins of VOCs (variant of concern) and potential drugs used in this study. </p>
Identification and Exploration of Immunity-Related Genes and Natural Products for Alzheimer's Disease Based on Bioinformatics, Molecular Docking and Molecular Dynamics
<p>Supplementary material to the article: Identification and Exploration of Immunity-Related Genes and Natural Products for Alzheimer’s Disease Based on Bioinformatics, Molecular Docking and Molecular Dynamics,These data are available to researchers.</p>
Figure 6 in Molecular docking studies and evaluation of the antiretroviral activity and cytotoxicity of the species Lafoensia pacari Saint-Hilaire
Figure 6. Structures of Ellagic Acid, Gallic Acid, α and β Punicalagins.
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OpenNeuro
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