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pymol program  (Accelrys)

 
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    Accelrys pymol program
    Pymol Program, supplied by Accelrys, 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+program/pymol/pmc12820053-144-11-17
    Average 86 stars, based on 1 article reviews
    pymol program - by Bioz Stars, 2026-09
    86/100 stars

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    other:

    Article Title: On-Resin DIAMSAR-Conjugated CD38-Targeted Peptides and Their Inverso and Dimeric-Inverso Analogs for PET Imaging of Multiple Myeloma.
    Article Snippet: CD38 is an established biomarker of multiple myeloma (MM), and peptide-based radiopharmaceuticals targeted to this receptor offer a route to molecularly specific imaging.. In this work, we identified a novel CD38-targeted peptide sequence (HAPWFRGGGGS) through phage display and synthesized it using automated solid-phase peptide synthesis.. The peptide was modified by introducing a PEG4 spacer and on-resin conjugation of the DIAMSAR chelator, which forms a stable complex with Copper64 (Cu-64), yielding DIAMSAR-PEG4-HAPWFRGGGGS (Monomer_L).

    Article Title: Evaluation of Ginsenosides and Their Derivatives From Panax ginseng as Aromatase Inhibitors for Breast Cancer Treatment—An in silico study
    Article Snippet: The contact between the ligands and the residues found within the active site of the protein, including the hydrogen bonds, hydrophobic contacts, and van der Waals, was identified using visualizing tools such as Pymol and BIOVIA Discovery Studio Version 2021 [ ].

    Article Title: Gut microbiota-derived xanthohumol protects against heatstroke by inhibiting macrophage pyroptosis in mice
    Article Snippet: Data was visualized using PyMOL (Accelrys, CA, USA).

    Article Title: On-Resin DIAMSAR-Conjugated CD38-Targeted Peptides and Their Inverso and Dimeric-Inverso Analogs for PET Imaging of Multiple Myeloma
    Article Snippet: Protein–ligand interactions were visualized using PyMol and Discovery Studio Visualizer (BIOVIA).

    Software:

    Article Title: Magnolia officinalis Rehder & E.H.Wilson. Bark Extract and Magnolol Alleviate Allergic Rhinitis via Modulating NF-κB/MAPK Signaling
    Article Snippet: Molecular docking was conducted utilizing the AutoDock Vina (version 1.2.0) software, in which lower binding energy values were indicative of more stable interactions. .. The results of the docking process were then rendered visually using the PyMol and Discovery Studio 4.5 software programs, which were developed by Accelrys Inc. (San Diego, CA, USA). .. Specific primers were designed, followed by the preparation of SYBR Green master mixes (YEASEN Biotch, Shanghai, China, #11120ES60) for qRT-PCR.

    Article Title: Magnolia officinalis Rehder & E.H.Wilson. Bark Extract and Magnolol Alleviate Allergic Rhinitis via Modulating NF-κB/MAPK Signaling.
    Article Snippet: Molecular docking was conducted utilizing the AutoDock Vina (version 1.2.0) software, in which lower binding energy values were indicative of more stable interactions. .. The results of the docking process were then rendered visually using the PyMol and Discovery Studio 4.5 software programs, which were developed by Accelrys Inc. (San Diego, CA, USA). .. Specific primers were designed, followed by the preparation of SYBR Green master mixes (YEASEN Biotch, Shanghai, China, #11120ES60) for qRT-PCR.

    Generated:

    Article Title: Beyond MIDAS: An In Silico Study of a Putative Noncanonical C16 Binding Site in αvβ3 Integrin
    Article Snippet: .. All figures and movies were generated using VMD (version 1.9.4a51), the open-source version of PyMol, BIOVIA Discovery Studio 2021, LigPlot, and SAMSON. ..

    Binding Assay:

    Article Title: NRF2-TERT-ACSL4 pathway inhibits ferroptosis and regulates cytoskeletal dynamics to mitigate ovarian aging.
    Article Snippet: This is a PDF of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability.. This version will undergo additional copyediting, typesetting and review before it is published in its final form.. As such, this version is no longer the Accepted Manuscript, but it is not yet the definitive Version of Record; we are providing this early version to give early visibility of the article.



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    program pymol  (DeLano Scientific)
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    a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program <t>PyMOL</t> <t>(DeLano</t> Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )
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    program pymol v2.3.4  (Schrodinger LLC)
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    a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program <t>PyMOL</t> <t>(DeLano</t> Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )
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    a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program <t>PyMOL</t> <t>(DeLano</t> Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )
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    Image Search Results


    a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program PyMOL (DeLano Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )

    Journal: Herz

    Article Title: Methamphetamine-induced cardiotoxicity: in search of protective transcriptional mechanisms

    doi: 10.1007/s00059-024-05279-6

    Figure Lengend Snippet: a Crystal structure of a parallel signal transducer and activator of transcription 3 ( STAT3 ) dimer bound to DNA in orthogonal views. The surface structure is colored according to atom type, with oxygen in red, nitrogen in blue, sulfur in dark yellow, and carbon in either bright yellow or green depending on the protomer. The double-helix structure of DNA is colored in cyan. The crystallographic data were taken from the Protein Data Bank (PDB) file 1BG1 for the STAT3 parallel dimer . b Ribbon diagram of an anti-parallel STAT3 dimer. The α‑helical coiled-coil domains are colored in yellow, the DNA-binding domains in cyan, the linker domains in green , and the SH2 domains in red. Structural data were from the PDB file 6TLC for STAT3 . Figures b and c were created with the program PyMOL (DeLano Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway. Binding of IL‑6 or a related cytokine to the heterodimeric cell surface receptor triggers a series of tyrosine-phosphorylation steps catalyzed by non-covalently bound Janus kinase ( JAK ), including JAK auto-phosphorylation and receptor phosphorylation. The phosphorylated receptor tail recruits STAT3 molecules, which are then phosphorylated at a single tyrosine ( 1 ). Through spontaneous dissociation and re-association, the activated STAT3 proteins constantly oscillate between a parallel and an antiparallel dimer conformation ( 2 ). After binding to importins ( 3 ), phospho-STAT3 dimers are imported into the nucleus via nuclear pore complexes ( 4 ). In the nucleus, STAT3 proteins modulate gene expression ( 5 ) and rearrange in an antiparallel dimer conformation ( 6 ) to be dephosphorylated ( 7 )

    Article Snippet: Figures b and c were created with the program PyMOL (DeLano Scientific). c Schematic model of the interleukin (IL)-6-induced JAK/STAT3 signaling pathway.

    Techniques: Binding Assay, Cell Surface Receptor Assay, Phospho-proteomics, Gene Expression