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pymol program  (SourceForge net)

 
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    Structured Review

    SourceForge net pymol program
    Pymol Program, supplied by SourceForge net, 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+program/program+pymol/pmc02597519-74-38-41
    Average 90 stars, based on 1 article reviews
    pymol program - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: CDH2 mutation affecting N-cadherin function causes attention-deficit hyperactivity disorder in humans and mice
    Article Snippet: PyMOL program ( https://sourceforge.net/projects/pymol/ ) was used to generate all structural figures .

    Sequencing:

    Article Title: Molecular characterization, developmental expression, and modulation of occludin by early intervention with Clostridium butyricum in Muscovy ducks.
    Article Snippet: .. Pymol program (http://pymol.sourceforge.net) was used to superimpose similarities between the predicted structure and template sequence. ..

    In Silico:

    Article Title: Analysis of ACE2 and TMPRSS2 coding variants as a risk factor for SARS‐CoV‐2 from 946 whole‐exome sequencing data in the Turkish population
    Article Snippet: .. PyMol program ( http://pymol.sourceforge.net ) was used to visualize and generate in silico mutant proteins. ..

    Mutagenesis:

    Article Title: Analysis of ACE2 and TMPRSS2 coding variants as a risk factor for SARS‐CoV‐2 from 946 whole‐exome sequencing data in the Turkish population
    Article Snippet: .. PyMol program ( http://pymol.sourceforge.net ) was used to visualize and generate in silico mutant proteins. ..



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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