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mestrenova mestrelab research s l  (Mestrelab Research)

 
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    Mestrelab Research mestrenova mestrelab research s l
    KEY RESOURCES TABLE
    Mestrenova Mestrelab Research S L, supplied by Mestrelab Research, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pymol+software+(python-based+molecular+visualization+system)/mestrenova/pmc06209319-362-254-255
    Average 86 stars, based on 1 article reviews
    mestrenova mestrelab research s l - by Bioz Stars, 2026-09
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    Images

    1) Product Images from "Structural and Biochemical Studies of Non-Native Agonists of the LasR Quorum Sensing Receptor Reveal an L3 Loop “Out” Conformation for LasR"

    Article Title: Structural and Biochemical Studies of Non-Native Agonists of the LasR Quorum Sensing Receptor Reveal an L3 Loop “Out” Conformation for LasR

    Journal: Cell chemical biology

    doi: 10.1016/j.chembiol.2018.06.007

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Virus, Recombinant, Software, Structural Proteomics

    Related Articles

    Software:

    Article Title: Solid dissolvable compositions comprising capsules
    Article Snippet: .. The samples are stored and processed using system software appropriate for NMR spectroscopy such as MestReNova version 12.0.4-22023 (available from Mestrelab Research) or equivalent. ..

    Article Title: 1 H-NMR metabolomic profiling of Methanobacterium and Methanosarcina reveals unusual intracellular trimethylamine and acetamide production.
    Article Snippet: The equipment was set to a proton frequency of 600.58 MHz, and measurements were 118 carried out at a temperature of 298 K. The spectra were recorded using pulse sequence zgesgp (in 119 Bruker notation), 256 scans were performed for each sample, with a relaxation delay of 3.5 s, 120 acquisition time 2.73 s, 64k points, spectrum width 20.0126 ppm. .. The spectra were then processed – 121 first, the spectrum phase was corrected using TopSpin 3.2 software (Bruker, GmBH, Germany) and the 122 baseline using the MestReNova 11.0.3 program (Mestrelab Research, S.L., Spain). ..

    Article Title: 1 H NMR-based machine learning methods for rapid authentication and composition profiling of crude palm oil.
    Article Snippet: A rapid analytical workflow for determining geographical origin and predicting fatty acid composition of crude palm oil (CPO) was developed using 1H NMR, GC-FID, and machine learning.. Analyzing CPO samples from Indonesia, Malaysia, the Philippines, and Thailand using unsupervised fingerprinting with principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) revealed partial origin-based grouping.. Supervised classification, validated via leave-one-out cross-validation (LOOCV) and uncertainty quantification (UQ), reliably discriminated the origins above random chance.

    Article Title: Complete NMR assignment for 275 of the most common dipeptides in intrinsically disordered proteins.
    Article Snippet: .. Spectra processing and assignments95 Acquired NMR spectra were processed using the MestReNova software (version 14.02.0-26256, Mestrelab Research) and96 referenced to DSS. ..

    Nuclear Magnetic Resonance:

    Article Title: Solid dissolvable compositions comprising capsules
    Article Snippet: .. The samples are stored and processed using system software appropriate for NMR spectroscopy such as MestReNova version 12.0.4-22023 (available from Mestrelab Research) or equivalent. ..

    Article Title: 1 H NMR-based machine learning methods for rapid authentication and composition profiling of crude palm oil.
    Article Snippet: A rapid analytical workflow for determining geographical origin and predicting fatty acid composition of crude palm oil (CPO) was developed using 1H NMR, GC-FID, and machine learning.. Analyzing CPO samples from Indonesia, Malaysia, the Philippines, and Thailand using unsupervised fingerprinting with principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) revealed partial origin-based grouping.. Supervised classification, validated via leave-one-out cross-validation (LOOCV) and uncertainty quantification (UQ), reliably discriminated the origins above random chance.

    Article Title: Complete NMR assignment for 275 of the most common dipeptides in intrinsically disordered proteins.
    Article Snippet: .. Spectra processing and assignments95 Acquired NMR spectra were processed using the MestReNova software (version 14.02.0-26256, Mestrelab Research) and96 referenced to DSS. ..

    Spectroscopy:

    Article Title: Solid dissolvable compositions comprising capsules
    Article Snippet: .. The samples are stored and processed using system software appropriate for NMR spectroscopy such as MestReNova version 12.0.4-22023 (available from Mestrelab Research) or equivalent. ..



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    pymol software (python-based molecular visualization system)  (DeLano Scientific)
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    Binding model of CHE19 to the CHIKV spike protein. (A) Amino acid (aa) sequence alignment (1 to 300 aa) using Blosum62 for E2 (423 aa) from the CHIKV Thai#16856, Thai/ES245-7, Ross, and Thai E2 mutants. Domains of E2 determined from the crystal structure of the E2/E1 heterodimer (16) are shown. Domains A, B, and C are shown in black with underlining, while the N-linker segment and 2 β-ribbon connectors, β-ribbon (1) and β-ribbon (2) are shown in purple. The amino acid residues of Thai#16856 came into contact within 4 Å from the heavy atoms of the paratopes of the CHE19, as in panel A-2, are shown in red. The positions where residues are replaced by alanine of the respective Thai E2 mutants, YKATR/AAATA, Thai/TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA, are shown in light blue. (B) Nucleotide and amino acid sequences of the Fab fragment region of the CHE19 light chain and heavy chain. PCR primer sequences are shown in red (sense) and blue (antisense). The signal peptide sequence of each chain is highlighted in yellow. Variable regions of the light chain and heavy chain are highlighted in light blue and blue, respectively. (C-1) Deduced binding model no. 16 of CHE19 to the CHIKV spike protein. Ribbon drawings of the spike with the bound Fab fragment of CHE19 and whole model of CHE19. The E1 glycoprotein is shown in red, the E2 glycoprotein in green, and the CHE19 Fab fragment region or whole Fab fragment plus Fc structure is shown in blue for the heavy chain and light blue for the light chain. The ribbon diagram of the spike protein was reconstructed by HMHC using PDB ID 6NK7, and the ribbon diagrams of CHE19 Fab fragment and Fab fragment-Fc were reconstructed using PDB IDs 5TL5 and 5TL5 to 1IGT, respectively. (C-2) Blowup of the binding location with the amino acids (shown as spheres) that are in contact within 4 Å from the heavy atoms of the paratopes of the CHE19 region. (C-3) The binding of CHE19 Fab fragment (translucent surface drawings: blue for the heavy chain and light blue for the light chain) on the E2-E1 heterodimer (E2, green ribbon; E1, red ribbon) overlapped the position where the E3 glycoprotein (pink ribbon) was originally occupied. The fusion loop located at the distal end of the E1 glycoprotein is shown in yellow. The ribbon diagrams of the E2-E1 heterodimer in panels C-2 and C-3 were reconstructed by HMHC using PDB ID 3N42. (C-4) Structural image showing that the CHE19 (surface drawings: blue for the heavy chain and light blue for the light chain) connects the CHIKV virion by binding to the spike protein (brown ribbon) existing on two different virions. The ribbon diagrams of structural proteins are reconstructed by HMHC using PDB ID 6NK7. The ratio between virion size and spike size was determined with reference to the mature CHIKV structure model (51). These images were visualized using the UCSF Chimera software (panels C-1, C-3, and C-4) and the <t>PyMOL</t> software (panel C-2). (D) Expression of CHIKV mutant E proteins and their detection by the respective MAbs. (D-1) MAb reactivities by IFA of 293T cells transfected with pCAGGS/CHIKV-E Thai#16856, pCAGGS/CHIKV-E Thai/ES245-7, and four pCAGGS/CHIKV mutant E expression plasmids, pCAGGS/CHIKV-E Thai/YKATR/AAATA, pCAGGS/CHIKV-E Thai/TTTDK/AAADA, pCAGGS/CHIKV-E Thai/HKKW/AAAA, and pCAGGS/CHIKV-E Thai/RQGK/AQGA, were probed with the respective MAbs and anti-CHIKV rabbit serum as a positive control. (D-2) Expression of CHIKV mutant E proteins in 293T cells transfected with the respective CHIKV-E-expressing vectors was detected by Western blotting using anti-CHIKV rabbit serum and two anti-CHIKV mouse IgGs, CHE15 and CHE22. The cellular beta-actin as an internal control was probed by anti-beta-actin mouse MAb (Sigma-Aldrich). (E) VSVΔG-luci pseudoviruses bearing the CHIKV-E protein of the Thai#16856, Thai/ES245-7, and Thai E2 mutants (YKATR/AAATA, TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA) were examined for their infectivity to Vero cells and their reactivity against CHE19. (E-1) Pseudotype viruses except VSVΔG-luci (CHIKV-E Thai E2 HKKW/AAAA) were produced, and their infectivity was inhibited by anti-CHIKV rabbit serum treatment (1:100). The infectivity of the respective pseudotype virus is shown as a percentage of the VSVΔG-luci (CHIKV-E Thai#16856) infectivity. (E-2) VSVΔG-luci (CHIKV-E Thai E2 YKATR/AAATA) was completely resistant against the CHE19 treatment (10 μg/ml), and VSVΔG-luci (CHIKV-E Thai E2 RQGK/AQGA) was partially resistant, but VSVΔG-luci (CHIKV-E Thai E2 TTTDK/AAADA) was neutralized to the same level as VSVΔG-luci (CHIKV-E Thai#16856). The infectivity of each pseudovirus is shown as a percentage of the infectivity of the respective pseudovirus treated with the Ctrl IgG. Data are the mean ± SEM (n = 6) of three independent experiments. Statistical significance was evaluated by an unpaired two-tailed t test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.
    Pymol Software (Python Based Molecular Visualization System), supplied by DeLano Scientific, 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/pymol+software+(python-based+molecular+visualization+system)/pymol+software/pmc07495367-645-26-32
    Average 90 stars, based on 1 article reviews
    pymol software (python-based molecular visualization system) - by Bioz Stars, 2026-09
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    Binding model of CHE19 to the CHIKV spike protein. (A) Amino acid (aa) sequence alignment (1 to 300 aa) using Blosum62 for E2 (423 aa) from the CHIKV Thai#16856, Thai/ES245-7, Ross, and Thai E2 mutants. Domains of E2 determined from the crystal structure of the E2/E1 heterodimer (16) are shown. Domains A, B, and C are shown in black with underlining, while the N-linker segment and 2 β-ribbon connectors, β-ribbon (1) and β-ribbon (2) are shown in purple. The amino acid residues of Thai#16856 came into contact within 4 Å from the heavy atoms of the paratopes of the CHE19, as in panel A-2, are shown in red. The positions where residues are replaced by alanine of the respective Thai E2 mutants, YKATR/AAATA, Thai/TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA, are shown in light blue. (B) Nucleotide and amino acid sequences of the Fab fragment region of the CHE19 light chain and heavy chain. PCR primer sequences are shown in red (sense) and blue (antisense). The signal peptide sequence of each chain is highlighted in yellow. Variable regions of the light chain and heavy chain are highlighted in light blue and blue, respectively. (C-1) Deduced binding model no. 16 of CHE19 to the CHIKV spike protein. Ribbon drawings of the spike with the bound Fab fragment of CHE19 and whole model of CHE19. The E1 glycoprotein is shown in red, the E2 glycoprotein in green, and the CHE19 Fab fragment region or whole Fab fragment plus Fc structure is shown in blue for the heavy chain and light blue for the light chain. The ribbon diagram of the spike protein was reconstructed by HMHC using PDB ID 6NK7, and the ribbon diagrams of CHE19 Fab fragment and Fab fragment-Fc were reconstructed using PDB IDs 5TL5 and 5TL5 to 1IGT, respectively. (C-2) Blowup of the binding location with the amino acids (shown as spheres) that are in contact within 4 Å from the heavy atoms of the paratopes of the CHE19 region. (C-3) The binding of CHE19 Fab fragment (translucent surface drawings: blue for the heavy chain and light blue for the light chain) on the E2-E1 heterodimer (E2, green ribbon; E1, red ribbon) overlapped the position where the E3 glycoprotein (pink ribbon) was originally occupied. The fusion loop located at the distal end of the E1 glycoprotein is shown in yellow. The ribbon diagrams of the E2-E1 heterodimer in panels C-2 and C-3 were reconstructed by HMHC using PDB ID 3N42. (C-4) Structural image showing that the CHE19 (surface drawings: blue for the heavy chain and light blue for the light chain) connects the CHIKV virion by binding to the spike protein (brown ribbon) existing on two different virions. The ribbon diagrams of structural proteins are reconstructed by HMHC using PDB ID 6NK7. The ratio between virion size and spike size was determined with reference to the mature CHIKV structure model (51). These images were visualized using the UCSF Chimera software (panels C-1, C-3, and C-4) and the PyMOL software (panel C-2). (D) Expression of CHIKV mutant E proteins and their detection by the respective MAbs. (D-1) MAb reactivities by IFA of 293T cells transfected with pCAGGS/CHIKV-E Thai#16856, pCAGGS/CHIKV-E Thai/ES245-7, and four pCAGGS/CHIKV mutant E expression plasmids, pCAGGS/CHIKV-E Thai/YKATR/AAATA, pCAGGS/CHIKV-E Thai/TTTDK/AAADA, pCAGGS/CHIKV-E Thai/HKKW/AAAA, and pCAGGS/CHIKV-E Thai/RQGK/AQGA, were probed with the respective MAbs and anti-CHIKV rabbit serum as a positive control. (D-2) Expression of CHIKV mutant E proteins in 293T cells transfected with the respective CHIKV-E-expressing vectors was detected by Western blotting using anti-CHIKV rabbit serum and two anti-CHIKV mouse IgGs, CHE15 and CHE22. The cellular beta-actin as an internal control was probed by anti-beta-actin mouse MAb (Sigma-Aldrich). (E) VSVΔG-luci pseudoviruses bearing the CHIKV-E protein of the Thai#16856, Thai/ES245-7, and Thai E2 mutants (YKATR/AAATA, TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA) were examined for their infectivity to Vero cells and their reactivity against CHE19. (E-1) Pseudotype viruses except VSVΔG-luci (CHIKV-E Thai E2 HKKW/AAAA) were produced, and their infectivity was inhibited by anti-CHIKV rabbit serum treatment (1:100). The infectivity of the respective pseudotype virus is shown as a percentage of the VSVΔG-luci (CHIKV-E Thai#16856) infectivity. (E-2) VSVΔG-luci (CHIKV-E Thai E2 YKATR/AAATA) was completely resistant against the CHE19 treatment (10 μg/ml), and VSVΔG-luci (CHIKV-E Thai E2 RQGK/AQGA) was partially resistant, but VSVΔG-luci (CHIKV-E Thai E2 TTTDK/AAADA) was neutralized to the same level as VSVΔG-luci (CHIKV-E Thai#16856). The infectivity of each pseudovirus is shown as a percentage of the infectivity of the respective pseudovirus treated with the Ctrl IgG. Data are the mean ± SEM (n = 6) of three independent experiments. Statistical significance was evaluated by an unpaired two-tailed t test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

    Journal: Journal of Virology

    Article Title: Anti-Chikungunya Virus Monoclonal Antibody That Inhibits Viral Fusion and Release

    doi: 10.1128/JVI.00252-20

    Figure Lengend Snippet: Binding model of CHE19 to the CHIKV spike protein. (A) Amino acid (aa) sequence alignment (1 to 300 aa) using Blosum62 for E2 (423 aa) from the CHIKV Thai#16856, Thai/ES245-7, Ross, and Thai E2 mutants. Domains of E2 determined from the crystal structure of the E2/E1 heterodimer (16) are shown. Domains A, B, and C are shown in black with underlining, while the N-linker segment and 2 β-ribbon connectors, β-ribbon (1) and β-ribbon (2) are shown in purple. The amino acid residues of Thai#16856 came into contact within 4 Å from the heavy atoms of the paratopes of the CHE19, as in panel A-2, are shown in red. The positions where residues are replaced by alanine of the respective Thai E2 mutants, YKATR/AAATA, Thai/TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA, are shown in light blue. (B) Nucleotide and amino acid sequences of the Fab fragment region of the CHE19 light chain and heavy chain. PCR primer sequences are shown in red (sense) and blue (antisense). The signal peptide sequence of each chain is highlighted in yellow. Variable regions of the light chain and heavy chain are highlighted in light blue and blue, respectively. (C-1) Deduced binding model no. 16 of CHE19 to the CHIKV spike protein. Ribbon drawings of the spike with the bound Fab fragment of CHE19 and whole model of CHE19. The E1 glycoprotein is shown in red, the E2 glycoprotein in green, and the CHE19 Fab fragment region or whole Fab fragment plus Fc structure is shown in blue for the heavy chain and light blue for the light chain. The ribbon diagram of the spike protein was reconstructed by HMHC using PDB ID 6NK7, and the ribbon diagrams of CHE19 Fab fragment and Fab fragment-Fc were reconstructed using PDB IDs 5TL5 and 5TL5 to 1IGT, respectively. (C-2) Blowup of the binding location with the amino acids (shown as spheres) that are in contact within 4 Å from the heavy atoms of the paratopes of the CHE19 region. (C-3) The binding of CHE19 Fab fragment (translucent surface drawings: blue for the heavy chain and light blue for the light chain) on the E2-E1 heterodimer (E2, green ribbon; E1, red ribbon) overlapped the position where the E3 glycoprotein (pink ribbon) was originally occupied. The fusion loop located at the distal end of the E1 glycoprotein is shown in yellow. The ribbon diagrams of the E2-E1 heterodimer in panels C-2 and C-3 were reconstructed by HMHC using PDB ID 3N42. (C-4) Structural image showing that the CHE19 (surface drawings: blue for the heavy chain and light blue for the light chain) connects the CHIKV virion by binding to the spike protein (brown ribbon) existing on two different virions. The ribbon diagrams of structural proteins are reconstructed by HMHC using PDB ID 6NK7. The ratio between virion size and spike size was determined with reference to the mature CHIKV structure model (51). These images were visualized using the UCSF Chimera software (panels C-1, C-3, and C-4) and the PyMOL software (panel C-2). (D) Expression of CHIKV mutant E proteins and their detection by the respective MAbs. (D-1) MAb reactivities by IFA of 293T cells transfected with pCAGGS/CHIKV-E Thai#16856, pCAGGS/CHIKV-E Thai/ES245-7, and four pCAGGS/CHIKV mutant E expression plasmids, pCAGGS/CHIKV-E Thai/YKATR/AAATA, pCAGGS/CHIKV-E Thai/TTTDK/AAADA, pCAGGS/CHIKV-E Thai/HKKW/AAAA, and pCAGGS/CHIKV-E Thai/RQGK/AQGA, were probed with the respective MAbs and anti-CHIKV rabbit serum as a positive control. (D-2) Expression of CHIKV mutant E proteins in 293T cells transfected with the respective CHIKV-E-expressing vectors was detected by Western blotting using anti-CHIKV rabbit serum and two anti-CHIKV mouse IgGs, CHE15 and CHE22. The cellular beta-actin as an internal control was probed by anti-beta-actin mouse MAb (Sigma-Aldrich). (E) VSVΔG-luci pseudoviruses bearing the CHIKV-E protein of the Thai#16856, Thai/ES245-7, and Thai E2 mutants (YKATR/AAATA, TTTDK/AAADA, HKKW/AAAA, and RQGK/AQGA) were examined for their infectivity to Vero cells and their reactivity against CHE19. (E-1) Pseudotype viruses except VSVΔG-luci (CHIKV-E Thai E2 HKKW/AAAA) were produced, and their infectivity was inhibited by anti-CHIKV rabbit serum treatment (1:100). The infectivity of the respective pseudotype virus is shown as a percentage of the VSVΔG-luci (CHIKV-E Thai#16856) infectivity. (E-2) VSVΔG-luci (CHIKV-E Thai E2 YKATR/AAATA) was completely resistant against the CHE19 treatment (10 μg/ml), and VSVΔG-luci (CHIKV-E Thai E2 RQGK/AQGA) was partially resistant, but VSVΔG-luci (CHIKV-E Thai E2 TTTDK/AAADA) was neutralized to the same level as VSVΔG-luci (CHIKV-E Thai#16856). The infectivity of each pseudovirus is shown as a percentage of the infectivity of the respective pseudovirus treated with the Ctrl IgG. Data are the mean ± SEM (n = 6) of three independent experiments. Statistical significance was evaluated by an unpaired two-tailed t test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

    Article Snippet: The obtained docking models of the CHE19 Fab fragment-CHIKV E2-E1 complex were examined to confirm that the paratope of the antibody interacts with the antigen by PyMOL software (Python-based molecular visualization system; Delano Scientific, San Francisco, CA).

    Techniques: Binding Assay, Sequencing, Software, Expressing, Mutagenesis, Transfection, Positive Control, Western Blot, Infection, Produced, Two Tailed Test