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program pymol  (Schrodinger LLC)

 
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    Schrodinger LLC program pymol
    Program Pymol, supplied by Schrodinger LLC, 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/pmc12153054-103-14-21
    Average 90 stars, based on 1 article reviews
    program pymol - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    other:

    Article Title: An anti-PD-1-GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy.
    Article Snippet: Figures were prepared using the program PyMOL (Schroedinger, LLC).

    Article Title: Quantitative regulation of the thermal stability of enveloped virus vaccines by surface charge engineering to prevent the self-aggregation of attachment glycoproteins
    Article Snippet: The protein structures were visualized using the PyMOL program (The PyMOL Molecular Graphics System, Version 1.1eval, Schrodinger, LLC).

    Article Title: Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
    Article Snippet: The Pymol (Schrodinger, LLC) program was used to show molecular graphics, structure superposition and RMSD calculation between two structures.

    Article Title: Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants
    Article Snippet: The Pymol (Schrodinger, LLC) program was used to show molecular graphics, structure superposition, and RMSD calculation between two structures.

    Generated:

    Article Title: Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants
    Article Snippet: .. All the graphics were 143 generated using the program PyMOL (Schrodinger, LLC). ..

    Article Title: MlaC belongs to a unique class of non-canonical substrate-binding proteins and follows a novel phospholipid-binding mechanism.
    Article Snippet: The outer membrane (OM) of Gram-negative bacteria acts as a formidable barrier against a plethora of detrimental compounds owing to its asymmetric nature.. This is because the OM possesses lipopolysaccharides (LPSs) in the outer leaflet and phospholipids (PLs) in the inner leaflet.. The maintenance of lipid asymmetry (Mla) system is involved in preserving the distribution of PLs in OM.

    Article Title: Coordinated subdomain movements of MlaC regulate ligand binding and transport
    Article Snippet: The α-helix curvatures of proteins were analyzed using the tool Bendix embedded in the program VMD , . .. The visualization of structures, their superimpositions, and molecular graphic figures were generated using the program PyMOL (The PyMOL Molecular Graphics System, Schrodinger, LLC). ..

    Article Title: Water-mediated structural rearrangement establishes active conformation of caspases for apoptosis and inflammation.
    Article Snippet: Caspases are cysteine-dependent aspartate-specific proteases that play a crucial role in apoptosis (or programmed cell death) and inflammation.. Based on their function, caspases are majorly categorized into apoptotic (initiator/apical and effector/executioner) and inflammatory caspases.. Caspases undergo transition from an inactive zymogen to an active caspase to accomplish their function.



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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