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web-based graphical user interface (gui) of dockingserver  (Virtua Drug)

 
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    Virtua Drug web-based graphical user interface (gui) of dockingserver
    Affinity purification of cellular targets of compound D. (A) Biotin linked to the R1 group of compound D. This compound was bound to streptavidin-agarose and used to affinity purify proteins from a trophozoite cell lysate. The only significant hit identified by LC-MS/MS was HSP90 (see Table S3 in the supplemental material). (B) Predicted interactions between compound D and PfHSP90. (C) Modeling of the most likely binding orientation of compound D to the ATP binding site of HSP90 was carried out using <t>DockingServer.</t> Residues predicted to form hydrogen bonds with compound D are labeled in green, while those predicted to form hydrophobic interactions are labeled in blue. (D) Recombinant PfHSP90 binds to compound D. Purified recombinant PfHSP90 and PfHSP90-NTD used in subsequent experiments are shown in the Coomassie-stained gels to the left of the figure. Changes in the tryptophan fluorescence (346 nm) of PfHSP90 were monitored in the presence of increasing amounts of compound D or 17-AAG. K d values were calculated for both full-length (FL) PfHSP90 and PfHSP90-NTD. Values in brackets are the standard errors (SE) of the means of triplicate measurements.
    Web Based Graphical User Interface (Gui) Of Dockingserver, supplied by Virtua Drug, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/web-based+graphical+user+interface/dockingserver/pmc04775997-135-12-14
    Average 90 stars, based on 1 article reviews
    web-based graphical user interface (gui) of dockingserver - by Bioz Stars, 2026-11
    90/100 stars

    Images

    1) Product Images from "Imidazopyridazine Inhibitors of Plasmodium falciparum Calcium-Dependent Protein Kinase 1 Also Target Cyclic GMP-Dependent Protein Kinase and Heat Shock Protein 90 To Kill the Parasite at Different Stages of Intracellular Development"

    Article Title: Imidazopyridazine Inhibitors of Plasmodium falciparum Calcium-Dependent Protein Kinase 1 Also Target Cyclic GMP-Dependent Protein Kinase and Heat Shock Protein 90 To Kill the Parasite at Different Stages of Intracellular Development

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.01748-15

    Affinity purification of cellular targets of compound D. (A) Biotin linked to the R1 group of compound D. This compound was bound to streptavidin-agarose and used to affinity purify proteins from a trophozoite cell lysate. The only significant hit identified by LC-MS/MS was HSP90 (see Table S3 in the supplemental material). (B) Predicted interactions between compound D and PfHSP90. (C) Modeling of the most likely binding orientation of compound D to the ATP binding site of HSP90 was carried out using DockingServer. Residues predicted to form hydrogen bonds with compound D are labeled in green, while those predicted to form hydrophobic interactions are labeled in blue. (D) Recombinant PfHSP90 binds to compound D. Purified recombinant PfHSP90 and PfHSP90-NTD used in subsequent experiments are shown in the Coomassie-stained gels to the left of the figure. Changes in the tryptophan fluorescence (346 nm) of PfHSP90 were monitored in the presence of increasing amounts of compound D or 17-AAG. K d values were calculated for both full-length (FL) PfHSP90 and PfHSP90-NTD. Values in brackets are the standard errors (SE) of the means of triplicate measurements.
    Figure Legend Snippet: Affinity purification of cellular targets of compound D. (A) Biotin linked to the R1 group of compound D. This compound was bound to streptavidin-agarose and used to affinity purify proteins from a trophozoite cell lysate. The only significant hit identified by LC-MS/MS was HSP90 (see Table S3 in the supplemental material). (B) Predicted interactions between compound D and PfHSP90. (C) Modeling of the most likely binding orientation of compound D to the ATP binding site of HSP90 was carried out using DockingServer. Residues predicted to form hydrogen bonds with compound D are labeled in green, while those predicted to form hydrophobic interactions are labeled in blue. (D) Recombinant PfHSP90 binds to compound D. Purified recombinant PfHSP90 and PfHSP90-NTD used in subsequent experiments are shown in the Coomassie-stained gels to the left of the figure. Changes in the tryptophan fluorescence (346 nm) of PfHSP90 were monitored in the presence of increasing amounts of compound D or 17-AAG. K d values were calculated for both full-length (FL) PfHSP90 and PfHSP90-NTD. Values in brackets are the standard errors (SE) of the means of triplicate measurements.

    Techniques Used: Affinity Purification, Liquid Chromatography with Mass Spectroscopy, Binding Assay, Labeling, Recombinant, Purification, Staining, Fluorescence

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    Article Snippet: Department of Maths and Science Education, Kırıkkale University, Yahşihan, Kırıkkale, Turkey Department of Basic Medical Science, Faculty of Medicine, Yozgat Bozok University, Yozgat, Turkey Department of Basic Pharmacy Sciences, Faculty of Pharmacy, Cumhuriyet University, Sivas, Turkey Department of Gastronomy, Faculty of Arts and Design, İstanbul Rumeli University, Silivri, İstanbul, Turkey Department of Chemistry and Chemical Processing Technologies, Yıldızeli Vocational School, Sivas Cumhuriyet University, Sivas, Turkey Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Istanbul Istinye University, Zeytinburnu, Istanbul, Turkey Department of Biotechnology, Faculty of Science, Bartın University, Bartın, Turkey Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey

    Article Title: HIF‑1α and RACGAP1 promote the progression of hepatocellular carcinoma in a mutually regulatory way
    Article Snippet: Protein-protein docking was performed using the Global RAnge Molecular Matching: Docking Web Server (release 306; Virtua Drug Ltd, http://www.dockingserver.com ) ( ).

    Article Title: Benzaldehyde derivatives with functional propargyl groups as α-glucosidase inhibitors
    Article Snippet: The benzaldehyde derivatives (1-6) containing one and/or two propargyl arm(s) attached to the phenolic hydroxyl oxygen atom on the ortho-, metaor para-positions of the aromatic ring were synthesized and characterized by spectral and microanalytical methods.. The molecular structures were of 1, 4-6 determined by the single crystal X-ray crystallography.. The benzaldehyde derivatives containing free phenolic groups involved intraand inter-molecular hydrogen bonding interactions.

    Article Title: High Throughput Virtual Screening and Molecular Dynamics Simulation for Identifying a Putative Inhibitor of Bacterial CTX-M-15
    Article Snippet: The docking results (notably the docked complex of the top screened out inhibitor, MCULE-1352214421-0-56 with the bacterial CTX-M-15 protein) were re-confirmed by two other platforms, namely “YASARA GLOBAL DOCKING” (included within licensed YASARA STRUCTURE) and licensed “DOCKINGSERVER” [Virtua Drug Ltd., Budapest, Hungary].

    Article Title: High Throughput Virtual Screening and Molecular Dynamics Simulation for Identifying a Putative Inhibitor of Bacterial CTX-M-15
    Article Snippet: Further, the docking results (notably for the docked complex of the top screened out inhibitor with the bacterial CTX-M-15 protein) were re-confirmed by two other platforms, namely “YASARA GLOBAL DOCKING” (included within licensed YASARA STRUCTURE) and licensed “DOCKINGSERVER” [Virtua Drug Ltd., Hungary].

    Article Title: HIF‑1α and RACGAP1 promote the progression of hepatocellular carcinoma in a mutually regulatory way.
    Article Snippet: Protein‐protein docking was performed using the Global RAnge Molecular Matching: Docking Web Server (release 306; Virtua Drug Ltd, http://www.dockingserver.com) (21).

    Article Title: The Major Cat Allergen Fel d 1 Binds Steroid and Fatty Acid Semiochemicals: A Combined In Silico and In Vitro Study
    Article Snippet: The protein dimer and ligand dataset were uploaded to the DockingServer ( https://www.dockingserver.com ; Virtua Drug, Hungary), a web-based interface module consisting of Gasteiger and PM6 semiempirical quantum-mechanical partial charge calculations to enhance the accuracy of docking output utilizing the AutoDock 4 method [ ].

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    Affinity purification of cellular targets of compound D. (A) Biotin linked to the R1 group of compound D. This compound was bound to streptavidin-agarose and used to affinity purify proteins from a trophozoite cell lysate. The only significant hit identified by LC-MS/MS was HSP90 (see Table S3 in the supplemental material). (B) Predicted interactions between compound D and PfHSP90. (C) Modeling of the most likely binding orientation of compound D to the ATP binding site of HSP90 was carried out using <t>DockingServer.</t> Residues predicted to form hydrogen bonds with compound D are labeled in green, while those predicted to form hydrophobic interactions are labeled in blue. (D) Recombinant PfHSP90 binds to compound D. Purified recombinant PfHSP90 and PfHSP90-NTD used in subsequent experiments are shown in the Coomassie-stained gels to the left of the figure. Changes in the tryptophan fluorescence (346 nm) of PfHSP90 were monitored in the presence of increasing amounts of compound D or 17-AAG. K d values were calculated for both full-length (FL) PfHSP90 and PfHSP90-NTD. Values in brackets are the standard errors (SE) of the means of triplicate measurements.
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    Affinity purification of cellular targets of compound D. (A) Biotin linked to the R1 group of compound D. This compound was bound to streptavidin-agarose and used to affinity purify proteins from a trophozoite cell lysate. The only significant hit identified by LC-MS/MS was HSP90 (see Table S3 in the supplemental material). (B) Predicted interactions between compound D and PfHSP90. (C) Modeling of the most likely binding orientation of compound D to the ATP binding site of HSP90 was carried out using DockingServer. Residues predicted to form hydrogen bonds with compound D are labeled in green, while those predicted to form hydrophobic interactions are labeled in blue. (D) Recombinant PfHSP90 binds to compound D. Purified recombinant PfHSP90 and PfHSP90-NTD used in subsequent experiments are shown in the Coomassie-stained gels to the left of the figure. Changes in the tryptophan fluorescence (346 nm) of PfHSP90 were monitored in the presence of increasing amounts of compound D or 17-AAG. K d values were calculated for both full-length (FL) PfHSP90 and PfHSP90-NTD. Values in brackets are the standard errors (SE) of the means of triplicate measurements.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Imidazopyridazine Inhibitors of Plasmodium falciparum Calcium-Dependent Protein Kinase 1 Also Target Cyclic GMP-Dependent Protein Kinase and Heat Shock Protein 90 To Kill the Parasite at Different Stages of Intracellular Development

    doi: 10.1128/AAC.01748-15

    Figure Lengend Snippet: Affinity purification of cellular targets of compound D. (A) Biotin linked to the R1 group of compound D. This compound was bound to streptavidin-agarose and used to affinity purify proteins from a trophozoite cell lysate. The only significant hit identified by LC-MS/MS was HSP90 (see Table S3 in the supplemental material). (B) Predicted interactions between compound D and PfHSP90. (C) Modeling of the most likely binding orientation of compound D to the ATP binding site of HSP90 was carried out using DockingServer. Residues predicted to form hydrogen bonds with compound D are labeled in green, while those predicted to form hydrophobic interactions are labeled in blue. (D) Recombinant PfHSP90 binds to compound D. Purified recombinant PfHSP90 and PfHSP90-NTD used in subsequent experiments are shown in the Coomassie-stained gels to the left of the figure. Changes in the tryptophan fluorescence (346 nm) of PfHSP90 were monitored in the presence of increasing amounts of compound D or 17-AAG. K d values were calculated for both full-length (FL) PfHSP90 and PfHSP90-NTD. Values in brackets are the standard errors (SE) of the means of triplicate measurements.

    Article Snippet: Docking calculations were performed using the web-based graphical user interface (GUI) of DockingServer by Virtua Drug (Budapest, Hungary) ( ).

    Techniques: Affinity Purification, Liquid Chromatography with Mass Spectroscopy, Binding Assay, Labeling, Recombinant, Purification, Staining, Fluorescence