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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/program+pymol/pymol/pmc12820053-144-11-17
    Average 86 stars, based on 1 article reviews
    pymol program - by Bioz Stars, 2026-10
    86/100 stars

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    Software:

    Article Title: Impact of isothiazolinone biocides on gonadal steroid production: Focus on 3β-hydroxysteroid dehydrogenase inhibition.
    Article Snippet: Isothiazolinone biocides have been widely used as disinfectants during the COVID-19 pandemic.. However, their effects on gonadal steroidogenesis remain unclear.. This study investigated the endocrine-disrupting potential of isothiazolinone biocides, focusing on their inhibition of gonadal 3β-hydroxysteroid dehydrogenases (3β-HSDs).

    Article Title: Integrated Computational and Experimental Identification of High-Affinity Aptamers for Aflatoxin B1 Detection
    Article Snippet: Aflatoxin B1 (AFB1) is one of the highly toxic and carcinogenic aflatoxins widely contaminating food and feed commodities.. Developing significantly specific and sensitive detection methods is critical for food security and environmental health.. In this study, an integrated computational and experimental approach was used to determine aptamers specific to AFB1.

    Article Title: Natural polyphenols naringin targeting GSK3β: an effective strategy for enhancing myoblast proliferation and myogenesis for cultured meat production
    Article Snippet: Cultured meat (CM) is an emerging technology for meat production by the cultivation of muscle satellite cells.. However, this technology faces a critical challenge: muscle satellite cells struggle to maintain their stemness during long-term culture, which severely limits their proliferation ability.. Consequently, developing safe and effective additives to promote the growth of myoblasts has become a key focus of current research.

    Article Title: ALS target-site mutations and overexpression synergistically enhance mesosulfuron resistance in Lolium perenne.
    Article Snippet: The invasive weed Lolium perenne (perennial ryegrass) poses a considerable threat to winter wheat crops in China and is hardly controlled by acetolactate synthase (ALS) inhibitors after years of application.. In this study, four L. perenne populations from different locations in Henan were collected to evaluate the mechanisms of target site resistance to mesosulfuron-methyl.. The resistant index (RI) of these four populations ranged from 122.73 to 149.26 compared to the susceptible population.

    Article Title: Biophysical and Computational Analysis of a Potent Antimalarial Compound Binding to Human Serum Albumin: Insights for Drug–Protein Interaction
    Article Snippet: Default parameters were utilized during the docking process, as outlined in AutoDock. .. Subsequently, the docking results were visualized using PyMOL version 3.1.0 and BIOVIA Discovery Studio software version 2025 SP1. ..

    Article Title: Introductory phytochemical analysis and bioactivity screening of Aaronsohnia factorovskyi aerial parts: Antioxidant, anti-inflammatory and antidiabetic insights.
    Article Snippet: .. Pymol software (https://pymol.org/) was used to convert pdbqt files to pdb format, followed by visualization of the interactions in 3D and 2D views using Biovia Discovery Studio visualizer v21.1.0.20298 (Dassault Systèmes Biovia Corp., USA). ..

    Binding Assay:

    Article Title: Computational insights into harmala alkaloids as novel antimalarial candidates against Plasmodium falciparum
    Article Snippet: .. The PyMOL v2.0 program and the BIOVIA Discovery Studio were used to examine and visualize binding locations. ..

    Article Title: ALS target-site mutations and overexpression synergistically enhance mesosulfuron resistance in Lolium perenne.
    Article Snippet: The invasive weed Lolium perenne (perennial ryegrass) poses a considerable threat to winter wheat crops in China and is hardly controlled by acetolactate synthase (ALS) inhibitors after years of application.. In this study, four L. perenne populations from different locations in Henan were collected to evaluate the mechanisms of target site resistance to mesosulfuron-methyl.. The resistant index (RI) of these four populations ranged from 122.73 to 149.26 compared to the susceptible population.



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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