Phyllanthus niruri meets serum albumin: raw data and code from a bilirubin–BSA optical assay and 7.2 µs of molecular dynamics with human serum albumin

This record contains the raw results, analysis outputs, and scripts of a study of Phyllanthus niruri L. and serum albumin, submitted to scientific journal. Two components, not linked by chemical identification, are provided: 1. Cell-free optical assay. Absorbance readings at 440 nm of a bilirubin–bovine serum albumin system tested with four root preparations (methanol, ethyl acetate, chloroform, and ethanol extracts) and the commercial comparator Liv52: six blocks, six time points (0–180 min), 144 sample and 36 control readings. The preparations were not chemically characterized. 2. Computational analyses with human serum albumin (HSA; PDB 8Q3F). Docking of 37 constituents reported for the species and bilirubin; 36 molecular dynamics trajectories of 200 ns (12 systems × 3 trajectories; 7.2 µs in total); MM-GBSA end-point energies (4,983 snapshots) with PCA, LDA, and PERMANOVA; 36 dynamic cross-correlation matrices and network analyses; DFT calculations for seven constituents; and ADMET and activity-spectrum predictions from seven web platforms. Contents 01_IN-VITRO — optical readings 02_MOLECULAR_DOCKING — SwissDock results 03_ADMET — SwissADME, ADMET-AI, ADMETlab 3.0, Deep-PK, ProTox-3.0 outputs 04_BIOLOGICAL_ACTIVITY — PASS Online and PASS-Target outputs 05_DINAMICA — molecular dynamics results and trajectory analyses (RMSD, Rg, SASA, RMSF, ligand RMSD, hydrogen bonds) 06_MMGBSA — gmx_MMPBSA results 07_LDA_PCA — multivariate analysis of the energy terms 09_DCCM — cross-correlation matrices and networks 10_DFT — ORCA results 11_CODIGO — scripts for all analyses (Python scripts and Jupyter notebooks) 01_lee2016.pdf — source review of the constituents Methods in brief. GROMACS 2023.4, ff14SB, TIP3P, GAFF2; gmx_MMPBSA v1.6.0; ORCA 6.1.1 (B3LYP-D4/def2-SVP, water); SwissDock 2024. A README.txt at the root describes every folder, script, and convention. Computational results are hypotheses about modeled interactions. Reuse of the data and scripts is welcome with citation of the article and of this record.