Simulation and Experimental Validation Data for the Discovery of Amyloid-Like Short Peptide Assembly Codes

This dataset supports the manuscript "Discovery of Amyloid-Like Short Peptide Assembly Codes via an Experimentally Validated Predictive Computational Platform" (Zheng, Huang, Sun, Tian, Lee & Han). It provides the coarse-grained/hybrid-resolution molecular dynamics (PACE force field) simulation results and the experimental characterization data used to discover and validate short (3-5 residue) amyloid-forming peptides. This is a data-only archive; all analysis code (the Uni-Mol machine learning model, PACE MD automation, and the FTIR/ThT analysis scripts used on the data below) is maintained separately on GitHub (see Related resources below). Contents: 01_simulation_results.zip — A single combined table (result.csv) of Aggregation propensity (AP) and Amyloid-Like Tendency (ALT) scores from exhaustive/extended PACE simulations of tripeptides (n=1,303), tetrapeptides (n=235), and pentapeptides (n=119), together with a single combined folder (pdb/) of the final-frame PDB structures of all 1,657 simulated assemblies. 02_synthesis_qc.zip — Certificates of Analysis (purity/TFA content) for the 60 tri-, tetra-, and pentapeptides custom-synthesized for experimental validation (20 tripeptides, 26 tetrapeptides, 14 pentapeptides). 03_source_data.zip — Figure-level source data for all main and supplementary figures (figures 2-7 and S1-S20), including per-peptide FTIR and ThT source data where applicable to a given figure. Related resources: PACE MD simulation automation: Tutorial_Automated_Peptide_MD_PACE Uni-Mol machine learning model (code, training data, and weights): Self_Assembling_Amyloid_Like_Peptides_Predictor FTIR deconvolution and ThT/FTIR spectral clustering scripts, bundled together with their compiled input/output data (FTIR beta-sheet content, ThT fluorescence enhancement for the 60 characterized peptides, and a worked example): Tutorial_FTIR_ThT_Analysis Additional raw spectroscopic (FTIR/ThT) and imaging (SEM, XRD) data beyond what is included in 03_source_data.zip are available from the corresponding authors upon reasonable request. Please cite the associated manuscript when using this dataset.