Code and processed data for: A Dry-Lab Framework Linking Cross-Cancer Multi-Omics Prioritization, Genome-Scale Metabolic Rerouting, and Structure-Aware Candidate Assessment in Endocrine-Relevant Cancers

This Zenodo record contains the scripts, processed result tables, supplementary benchmark datasets, environment snapshots, and terminal logs supporting the manuscript: “A Dry-Lab Framework Linking Cross-Cancer Multi-Omics Prioritization, Genome-Scale Metabolic Rerouting, and Structure-Aware Candidate Assessment in Endocrine-Relevant Cancers”. The study was designed as a dry-lab framework integrating public multi-omics datasets, genome-scale metabolic modeling, external validation, LINCS-based perturbational support, and downstream structure-aware candidate assessment in endocrine-relevant cancers, with prostate adenocarcinoma (PRAD) as the primary disease context and breast cancer (BRCA) as the comparative context. To remain within Zenodo file-count limits while preserving usability, the deposited materials are provided mainly as category-level ZIP archives rather than as a large number of separate files. The README file is provided as an uncompressed text document for immediate inspection. Each ZIP archive groups closely related files belonging to one analytical module, including multi-omics analysis, external validation, genome-scale metabolic modeling robustness analyses, LINCS-based perturbational support, SLC16A1 docking and benchmark outputs, SLC25A1 exploratory docking outputs, molecular dynamics and MM/GBSA analyses, prediction-based ADMET/toxicity triage, scripts, logs, and environment snapshots. The deposited materials include:(1) processed multi-omics tables for PRAD, BRCA, and merged analyses;(2) external validation outputs from BRCA_METABRIC and PRAD_SU2C;(3) genome-scale metabolic modeling robustness summaries, reaction-proxy maps, and blocked-precursor diagnostics;(4) GSE92742-only LINCS perturbational-support outputs for SLC16A1;(5) SLC16A1 redocking, comparator, active-decoy benchmark, reranking, and consensus-scoring outputs;(6) SLC25A1 exploratory docking summaries and cross-box evaluation outputs;(7) processed source data for the matched 10 ns triplicate SLC16A1 MD/MM-GBSA analysis supporting Figure 4, Table S10, and Table S11;(8) processed source data for the initial 100 ps short-relaxation/MM-GBSA screening analysis supporting Table S8;(9) source tables and input files for the prediction-based physicochemical, ADMET, and toxicity triage supporting Table 7 and Tables S9A-S9C;(10) Python, R, and shell scripts used for analysis and table generation;(11) terminal log files documenting major analytical steps; and(12) environment snapshots for the primary reproducible conda environments, including uroc_v3, uroc_gem, and uroc_md, together with system-level R and software snapshots. This updated version adds reproducibility materials for the SLC16A1 molecular dynamics and MM/GBSA branch, the initial 100 ps short-relaxation/MM-GBSA screening analysis, prediction-based ADMET/toxicity triage, associated scripts, terminal logs, and the uroc_md software environment. The final primary extended-MD dataset in the manuscript is the matched 10 ns triplicate MD/MM-GBSA analysis of AZD3965/CHEMBL3335793 and CHEMBL3817902. The earlier 100 ps analyses are provided as initial short-relaxation/MM-GBSA screening data. Some internal run directories and script names contain historical labels such as “long” or “long-MD”; in this archive and in the manuscript, these labels should be interpreted as historical run labels for the initial 100 ps screening stage, not as the final primary extended-MD dataset. Raw public datasets were not re-deposited in this record and should be obtained from their original sources, including GDC/TCGA-PRAD, GDC/TCGA-BRCA, GTEx, PDC/CPTAC, Metabolomics Workbench, cBioPortal/METABRIC, SU2C PRAD, LINCS GSE92742, ChEMBL, Open Targets, and Human1/Human-GEM, as described in the manuscript and Supplementary Information. This record is deposited as a restricted-access reviewer package. Access to the deposited files may be provided to journal editors and reviewers through a reviewer-specific access link during peer review. If the manuscript is accepted or if the authors decide to make the archive publicly available, this record may be released as an open-access version while preserving the versioned DOI history. The 20260605 update further adds an integrated README and source-data package for the GEM targeted flux heatmaps shown in Figure 2 and Figure S1. The file README_Zenodo_20260605_integrated.md supersedes the earlier README files and provides the current archive-level guide, including a figure/table source-data crosswalk. The file figure_source_data_gem_heatmaps_20260605.zip contains PRAD/BRCA single-KO and double-KO targeted flux heatmap matrices, fixed-order heatmap matrices, generated heatmap images, and plotting scripts supporting Figure 2, Figure S1, Table 2, Table 3, Table S1, and Table S2.