LlewynLuo/RNAmd-v1

RNAmd v1

RNAmd is a public dataset of standardized RNA molecular-dynamics simulations, RNA dynamic labels, quality-control summaries and benchmark-ready metadata for compact functional and structured RNAs.

This Hugging Face Dataset repository is the core archival mirror for RNAmd v1. It mirrors the analysis-ready metadata, labels, QC summaries, protocol files, website index and RNA-only structures. The canonical RNAmd release server remains the primary access point for processed XTC trajectories and MP4 motion previews: https://rnamd.net/release.

Contents

Layer	Path	Status
Manifest, labels, QC and download lists	core/	complete
Website JSON index	web_data/	complete
RNA-only repaired PDB structures	structures/rna_only_pdb/	882 entries
Processed RNA-only 100 ps XTC trajectories	https://rnamd.net/release/trajectories/primary_xtc_100ps_rna_only/	882 entries on the canonical release server
Dynamics preview MP4 files	https://rnamd.net/release/visualizations/dynamics_preview/	882 samples on the canonical release server
Reproducibility protocol and workflow files	protocol/	included

Current release counts

• Samples: 882
• Completed 100 ns MD simulations: 882
• Raw full-system TRR entries available in the server archive: 882
• Processed public XTC files available from the canonical RNAmd server: 882
• Dynamics preview samples available from the canonical RNAmd server: 882
• Hugging Face mirror role: core analysis files, protocol, structures, website index and URL lists

Trajectory policy

All entries in the manifest correspond to completed 100 ns RNA MD simulations. The raw full-system TRR archive is not included in this public upload package because it is too large for the compact public v1 release. Raw archive availability is recorded in core/raw_archive_policy_v1.csv and in core/manifest_v1.csv.

The default public trajectory product is the processed RNA-only, PBC-processed, 100 ps stride XTC file. These files are distributed as direct per-sample downloads from the canonical RNAmd release server and are listed in core/download_urls_primary_trajectories_v1.txt.

Minimal usage

import pandas as pd

manifest = pd.read_csv("core/manifest_v1.csv")
residue = pd.read_csv("core/residue_flexibility_labels_v1.csv.gz")
contacts = pd.read_parquet("core/contact_persistence_labels_v1.parquet")

For samples with processed XTC available:

import MDAnalysis as mda

u = mda.Universe(
    "https://rnamd.net/release/trajectories/primary_structures/17RA.gro",
    "https://rnamd.net/release/trajectories/primary_xtc_100ps_rna_only/17RA.xtc",
)
print(len(u.trajectory))

File integrity

Use checksums_sha256_upload.txt for package-level integrity checks and core/upload_file_inventory_v1.csv for file sizes, roles and SHA-256 hashes.

Citation

RNAmd derives static structures from the Protein Data Bank. Users should cite the original PDB entries and the RNAmd database article once available.