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Traceable Claims in Bioinformatics

See what computational analyses actually reported, with provenance for every claim.Know what the science actually supports before you trust the answer.

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     Long Response


    Visualize Proteins: Interactive Transmission Network

    Visual first then explain. Top panels show 3D protein renders and an interactive transmission network connecting protein hubs across compartments; lower panels show quantitative graphs and a directed knowledge network. All claims cite sources below each figure.

    3D Protein Views (CD79A and GRIA2)

    Click and drag to rotate; use scroll to zoom. Structures loaded from PDB/AlphaFold where available and colored to highlight predicted ligand pockets and key residues from molecular dynamics decompositions reported in the integrated MS/MD study.

    CD79A: PBMC B cell receptor hub reported as a top peripheral target in integrated blood brain transcriptomics study. Docking and MD identified stable interactions with niraparib and icotinib with key residues LEU70 TRP76 PRO78 driving binding energetics
    Source:
    GRIA2: cortical glutamatergic hub identified in MS lesion transcriptomes; MD showed stable ligand interactions and key residues THR91 MET196 GLU193 ARG96 GLY62 contribute to binding energy decomposition
    Source:

    Interactive Transmission Network between Proteins

    Network shows directed edges from peripheral immune hub CD79A to central neural hub GRIA2 representing the conceptual transmission of perturbation or therapeutic dual targeting across compartments. Edge widths reflect STRING confidence and MD docking energy proxies.

    Quantitative Figures

    Data Table: Key MD and Docking Values

    ProteinLigandDocking kcal molMD RMSD nm meanKey residues
    CD79AIcotinib-6.30.18LEU70 TRP76 PRO78
    CD79ANiraparib-6.60.12LEU70 TRP76 PRO78
    GRIA2Icotinib-8.20.20THR91 MET196 GLU193 ARG96 GLY62
    GRIA2Niraparib-7.90.11THR91 MET196 GLU193 ARG96 GLY62
    Caveats and Limitations
    • Transcriptomic hubs come from small microarray cohorts (PBMCs 14 MS vs 15 controls brain lesions 5 vs 2) which increases sampling uncertainty and requires replication
    • Docking and MD suggest plausible binding but do not prove functional modulation; MM PBSA energy decomposition and per residue maps are helpful but inferential.
    • Protein structures: where experimental PDBs lack coverage, AlphaFold models can be used but carry prediction uncertainty for binding sites.
    Notes: Visualizations use public datasets and published MD/docking results; interpret networks as hypothesis generators requiring experimental follow up.


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    Updated: January 11, 2026

     Top Data Sources ExportMCP


     Analysis Wizard



    Preparing an automated pipeline that is aligning GEO microarray datasets GSE21942 GSE38010 running limma WGCNA and building STRING PPI to identify cross compartment hubs, followed by docking candidate ligands and running short MD and MM PBSA for ranking.



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    Visualize Proteins: Create Interactive Transmission Network Science Art

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