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    DeLano Scientific pymol
    Pymol, 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/pmc03169952-78-0-7
    Average 90 stars, based on 1 article reviews
    pymol - by Bioz Stars, 2026-09
    90/100 stars

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    other:

    Article Title: Elucidating the taste profile in black tea through molecular docking and molecular sensory science.
    Article Snippet: Crush-tear-curl (CTC) black tea is the largest global tea category by trade volume.. This study investigated the material basis for taste differences in CTC black tea through the analysis of electronic tongue, high-performance liquid chromatography, and high-speed amino acid analyzers.. Taste contributions were calculated using threshold values and dose-over-threshold calculations, then compounds were validated through recombination, addition, and omission experiments to confirm their contributions.

    Article Title: Shifts in bee diet breadths are associated with gene gains and losses and positive selection across olfactory receptors.
    Article Snippet: We then used TM-align and PyMOL v.2.6 (DeLano Scientific; San Francisco, CA, USA) to compare structures of de-novo and reference structural models (Zhang and Skolnick 2005) and calculated root mean squared deviation (RMSD) values between pairs of atoms.

    Article Title: Camellia Japonica Radix modulates gut microbiota and 9(S)-HpODE-mediated ferroptosis to alleviate oxidative stress against MASLD.
    Article Snippet: Background: Camellia japonica radix (CJR), derived from the root of Camellia japonica L., has the potential to function as an herbal tea substitute for the prevention and intervention of metabolic dysfunction-associated steatotic liver disease (MASLD).. It can provide systemic therapeutic benefits, boast a favorable safety profile, facilitate convenient consumption, and support long-term applicability.. Despite its potential, research on CJR

    Article Title: Cytochrome P450 Enzyme-Mediated Enantioselective Biotransformation of Chiral Fungicide Tebuconazole in Earthworm.
    Article Snippet: 157 In terms of molecular docking, Autodock Vina and PyMol (DeLano Scientific, Palo Alto, CA, 8 158 USA) were employed.

    Generated:

    Article Title: Transfer RNA Recognition Mechanism of Thermoplasma acidophilum Trm56, a SPOUT tRNA Methyltransferase that Possesses an Unusually Long C-terminal Region.
    Article Snippet: Trm56 from Thermoplasma acidophilum is an exceptional SpoU-TrmD superfamily enzyme, which possesses an unusually long C-terminal region, and catalyzes methylation of 2 -OH of ribose of C56 in tRNA.. T. acidophilum Trm56 methylates elongator tRNA (tRNA e) transcript effectively, however this enzyme methylates tRNA transcript slowly.. This enzymatic feature is common in T. acidophilum Trm56 and Pyrococcus horikoshii Trm56, which possesses a short C-terminal region.


    Produced:

    Article Title: Identification of uranyl-binding proteins in Arabidopsis thaliana cells exposed to uranium: Insights from a metalloproteomic analysis and characterization of Glycine-Rich RNA-binding protein 7 (GRP7).
    Article Snippet: .. The model was obtained using Alphafold v2.0 and the image was produced using PyMOL (DeLano Scientific, SanCarlos, CA, USA) as a ribbon model colored in the “chainbows” mode. ..

    Article Title:
    Article Snippet: .. Figures were produced using PyMOL (DeLano Scientific, San Carlos, CA, 208 USA). ..



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    pymol software (python-based molecular visualization system)  (DeLano Scientific)
    90
    DeLano Scientific pymol software (python-based molecular visualization system)
    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
    90/100 stars
    		  Buy from Supplier

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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