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    DeLano Scientific pymol version 0.97
    Pymol Version 0.97, 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+v0+99/pm21638595-46-0-3
    Average 90 stars, based on 1 article reviews
    pymol version 0.97 - by Bioz Stars, 2026-09
    90/100 stars

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    Article Title: DNA Topoisomerase Targeting Chemotherapeutics: What’s New?
    Article Snippet: All structure figures were generated using MacPyMol 0.99rc6 (DeLano Scientific, San Carlos, CA). b) Schematic representation of eukaryotic DNA topoisomerase I (TOP1B) catalytic cycle where the covalent enzyme-DNA intermediate constitutes the sole cellular target of camptothecin (CPT).

    Article Title: In silico study of potential antiviral activity of copper(II) complexes with non–steroidal anti–inflammatory drugs on various SARS–CoV–2 target proteins
    Article Snippet: DeLano, The PyMol Molecular Graphics System 0.99, DeLano Scientific, San Carlos, CA, USA, 2006.

    Article Title: Exploration of the SAR Connection between Morphinan- and Arylacetamide-Based κ Opioid Receptor (κOR) Agonists Using the Strategy of Bridging.
    Article Snippet: κ opioid receptor (κOR) is a subtype of opioid receptors, and there are two major κOR agonists currently available, morphinans and arylacetamides, which are structurally distinct from each other.. Numerous efforts had been made to correlate these series of compounds in order to establish a consensus binding pattern for κOR agonists.. Unfortunately, no morphinan-based agent with an arylacetamidyl substituent has been identified as a κOR agonist with a pharmacological profile similar to arylacetamides.

    Article Title: Design, Synthesis, Antifungal Evaluation, Structure–Activity Relationship (SAR) Study, and Molecular Docking of Novel Spirotryprostatin A Derivatives
    Article Snippet: PyMOL (version 0.99; DeLano Scientific, San Carlos, CA, USA) and ligplus v1.4.5 were used to view the graphic.

    Article Title: Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme.
    Article Snippet: d-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins.. Recently, radical S-adenosyl-l-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs.. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown.

    Article Title: Inhibition of Cancer Cell Proliferation and Bacterial Growth by Silver(I) Complexes Bearing a CH 3 -Substituted Thiadiazole-Based Thioamide.
    Article Snippet: The PyMOL Molecular Graphics System 0.99; DeLano Scientific: San Carlos, CA, USA, 2006.

    Article Title: N-acetyl-cysteine in combination with celecoxib inhibits Deoxynivalenol induced skin tumor initiation via induction of autophagic pathways in swiss mice.
    Article Snippet: Deoxynivalenol is a trichothecene mycotoxin which naturally contaminates small grain, cereals intended for human and animal consumption.. Investigations for dermal toxicity of DON has been needed and highlighted by WHO.. Previous studies on dermal toxicity suggest that DON has DNA damaging potential leading to skin tumor initiation in mice skin.

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    Article Title: Anti-Postmenopausal osteoporosis effects of Isopsoralen: A bioinformatics-integrated experimental study.
    Article Snippet: Funding information Important Science Fund of Science and Technology Bureau of Liaoning Province, Grant/Award Number: 2020JH2/10300056; National Natural Science Foundation of China, Grant/Award Number: 82073851 Abstract Isopsoralen (IPRN), which comes from the fruit of Psoralea corylifolia, has been identified as a kind of phytoestrogen and has been proven to be effective for the treatment of osteoporosis (OP).. However, the mechanisms underlying IPRN's anti-OP effects, especially the anti-postmenopausal osteoporosis (PMOP) effects, remain indistinct.. Thus, this study aimed to investigate the effects and mechanisms of IPRN's antiPMOP activity.



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    pymol software (python-based molecular visualization system)  (DeLano Scientific)
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    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