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… See the full description on the dataset page: https://huggingface.co/datasets/LlewynLuo/RNAmd-v1.
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1{2 "contact_entropy_mean": "0.0675263548899982",3 "contact_persistence_mean": "0.2266666666666666",4 "dynamic_qc_status": "ready",5 "dynamics_preview_gif_path": "",6 "dynamics_preview_mp4_path": "visualizations/dynamics_preview/2LP9.mp4",7 "dynamics_preview_status": "ready",8 "family_group": "short_structured_RNA_unresolved_lt25",9 "high_quality_flag": "yes",10 "label_8class": "other",11 "md_simulation_status": "complete_100ns",12 "method": "Solution NMR",13 "original_main_type": "short_structured_RNA_unresolved",14 "p_adaptability_mean": "2.2764079252878826",15 "p_rmsf_mean": "2.0972071170806883",16 "pdb_id": "2LP9",17 "primary_xtc_100ps_rna_only_path": "trajectories/primary_xtc_100ps_rna_only/2LP9.xtc",18 "primary_xtc_status": "ready",19 "priority_tier": "non_priority",20 "resolution": "",21 "rfam": "",22 "rg_mean": "2.4886504098161404",23 "rmsd_mean": "3.070016860961914",24 "rna_only_pdb_path": "structures/rna_only_pdb/2LP9.pdb",25 "rna_type": "viral regulatory RNA",26 "rna_type_confidence": "medium",27 "rna_type_evidence": "Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus | The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter. | short_structured_RNA_unresolved",28 "rna_type_source": "RCSB/PDB metadata keyword rule",29 "sequence": "GAGGACAUAGAUCUUC",30 "size_nt": "16.0",31 "source_pdb_url": "https://www.rcsb.org/structure/2LP9",32 "standardized_name": "",33 "traj_frames_used": "10",34 "traj_failed": "0",35 "rmsd_std": "1.0239667892456057",36 "rmsd_max": "3.4770493507385254",37 "rg_std": "0.0054842613846596",38 "rg_min": "2.478155032530437",39 "rg_max": "2.4979852567292995",40 "conformational_variability": "1.0294510506302652",41 "contact_persistence_std": "0.3995870884673843",42 "contact_entropy_max": "1.0",43 "misato_frames_used": "10.0",44 "misato_failed": "0.0",45 "misato_p_atom_count": "15.0",46 "p_adaptability_std": "0.5374574880191428",47 "p_adaptability_min": "1.440666913986206",48 "p_adaptability_q25": "1.8218804001808169",49 "p_adaptability_median": "2.3859992027282715",50 "p_adaptability_q75": "2.7029528617858887",51 "p_adaptability_max": "3.0923819541931152",52 "p_rmsf_std": "0.2830864454404386",53 "p_rmsf_min": "1.5442465543746948",54 "p_rmsf_q25": "1.8901140689849851",55 "p_rmsf_median": "2.0768918991088867",56 "p_rmsf_q75": "2.310439109802246",57 "p_rmsf_max": "2.5523955821990967",58 "p_high_adapt_frac_0p2nm": "1.0",59 "p_high_adapt_frac_0p4nm": "1.0",60 "base_centroid_adaptability_mean": "2.934232281499669",61 "base_centroid_adaptability_std": "0.5421832775256124",62 "base_centroid_adaptability_min": "0.9592100977897644",63 "base_centroid_adaptability_q25": "2.536028385162353",64 "base_centroid_adaptability_median": "2.903060913085937",65 "base_centroid_adaptability_q75": "3.2924695014953613",66 "base_centroid_adaptability_max": "5.0372514724731445",67 "adjacent_p_distance_std_mean": "0.5774837925231883",68 "adjacent_p_distance_std_std": "0.2002776897312011",69 "adjacent_p_distance_std_min": "0.0270999688655138",70 "adjacent_p_distance_std_q25": "0.5095259100198746",71 "adjacent_p_distance_std_median": "0.5516513586044312",72 "adjacent_p_distance_std_q75": "0.7481741309165955",73 "adjacent_p_distance_std_max": "0.8322229981422424",74 "adjacent_p_distance_mean": "0.8860309720039368",75 "long_contact_persistence_mean": "0.0282051282051282",76 "long_contact_persistence_std": "0.0449998173712416",77 "long_contact_persistence_min": "0.0",78 "long_contact_persistence_q25": "0.0",79 "long_contact_persistence_median": "0.0",80 "long_contact_persistence_q75": "0.1",81 "long_contact_persistence_max": "0.1",82 "long_contact_switching_mean": "0.1015384615384615",83 "long_contact_switching_std": "0.1619993425364699",84 "long_contact_switching_min": "0.0",85 "long_contact_switching_q25": "0.0",86 "long_contact_switching_median": "0.0",87 "long_contact_switching_q75": "0.36",88 "long_contact_switching_max": "0.36",89 "long_contact_entropy_mean": "0.1322810096039906",90 "long_contact_entropy_max": "0.4689955935892812",91 "stable_long_contact_frac": "0.0",92 "transient_long_contact_frac": "0.0",93 "initial_long_contact_frac": "0.0",94 "lost_initial_contact_frac": "0.0",95 "gained_contact_frac": "0.0"96}97