{"feature_sets":[{"about":"Size, shape, secondary structure, contacts, confidence and GSA composition of a protein chain with coordinates","features":[{"name":"residues","group":"size","unit":"residues","description":"Residues with CA coordinates"},{"name":"radius_of_gyration","group":"shape","unit":"Å","description":"Radius of gyration of the CA atoms"},{"name":"rg_relative","group":"shape","unit":"ratio","description":"Radius of gyration over that of a compact chain of the same length, 2.2·N^0.38 Å; near 1 for a compact globule, larger for extended or multi-domain chains","reference":"Skolnick, Kolinski & Ortiz (1997) J Mol Biol 265:217"},{"name":"asphericity","group":"shape","description":"Relative shape anisotropy κ² of the CA gyration tensor: 0 for a sphere, 1 for a rod","reference":"Theodorou & Suter (1985) Macromolecules 18:1206"},{"name":"max_dimension","group":"shape","unit":"Å","description":"Largest distance between two CA atoms"},{"name":"end_to_end_distance","group":"shape","unit":"Å","description":"Distance between the first and the last CA atom"},{"name":"helix_fraction","group":"secondary","unit":"fraction","description":"Fraction of residues TM-align assigns to a helix (H)","reference":"Zhang & Skolnick (2005) Nucleic Acids Res 33:2302 (TM-align secondary structure from CA distances)"},{"name":"strand_fraction","group":"secondary","unit":"fraction","description":"Fraction of residues TM-align assigns to a strand (E)","reference":"Zhang & Skolnick (2005) Nucleic Acids Res 33:2302 (TM-align secondary structure from CA distances)"},{"name":"turn_fraction","group":"secondary","unit":"fraction","description":"Fraction of residues TM-align assigns to a turn (T)","reference":"Zhang & Skolnick (2005) Nucleic Acids Res 33:2302 (TM-align secondary structure from CA distances)"},{"name":"coil_fraction","group":"secondary","unit":"fraction","description":"Fraction of residues TM-align assigns to coil (C)","reference":"Zhang & Skolnick (2005) Nucleic Acids Res 33:2302 (TM-align secondary structure from CA distances)"},{"name":"helix_segments","group":"secondary","unit":"count","description":"Helices: runs of 3 or more H residues (helices of about 7 residues and more)","reference":"Zhang & Skolnick (2005) Nucleic Acids Res 33:2302 (TM-align secondary structure from CA distances)"},{"name":"strand_segments","group":"secondary","unit":"count","description":"Strands: runs of 2 or more E residues (strands of about 6 residues and more)","reference":"Zhang & Skolnick (2005) Nucleic Acids Res 33:2302 (TM-align secondary structure from CA distances)"},{"name":"contacts_per_residue","group":"contacts","unit":"contacts/residue","description":"CA–CA contacts per residue","reference":"CA–CA distance below 8 Å, sequence separation 6 or more (CASP ranges: medium 12–23, long 24+)"},{"name":"medium_range_contact_fraction","group":"contacts","unit":"fraction","description":"Fraction of contacts at a sequence separation of 12 to 23","reference":"CA–CA distance below 8 Å, sequence separation 6 or more (CASP ranges: medium 12–23, long 24+)"},{"name":"long_range_contact_fraction","group":"contacts","unit":"fraction","description":"Fraction of contacts at a sequence separation of 24 or more","reference":"CA–CA distance below 8 Å, sequence separation 6 or more (CASP ranges: medium 12–23, long 24+)"},{"name":"relative_contact_order","group":"contacts","unit":"fraction","description":"Relative contact order: mean sequence separation of the contacts over the chain length (CA contacts as defined here)","reference":"Plaxco, Simons & Baker (1998) J Mol Biol 277:985"},{"name":"absolute_contact_order","group":"contacts","unit":"residues","description":"Absolute contact order: mean sequence separation of the contacts","reference":"Ivankov et al. (2003) Protein Sci 12:2057"},{"name":"chain_breaks","group":"quality","unit":"count","description":"Consecutive CA atoms more than 4.3 Å apart (missing residues)"},{"name":"mean_b","group":"quality","unit":"Ų or pLDDT","description":"Mean B-factor of the CA atoms; for predicted models, the mean pLDDT"},{"name":"std_b","group":"quality","unit":"Ų or pLDDT","description":"Standard deviation of the CA B-factors (pLDDT for predicted models)"},{"name":"predicted","group":"quality","unit":"flag","description":"1 when the structure is a computed model (B-factors are then pLDDT)"},{"name":"low_confidence_fraction","group":"quality","unit":"fraction","description":"Predicted models: fraction of residues with pLDDT below 70; 0 for experimental structures","reference":"AlphaFold DB confidence bands"},{"name":"gsa_entropy_bits","group":"gsa","unit":"bits","description":"Shannon entropy of the chain's GSA state composition"},{"name":"gsa_a","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state a","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_b","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state b","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_c","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state c","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_d","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state d","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_e","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state e","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_f","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state f","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_g","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state g","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_h","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state h","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_i","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state i","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_j","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state j","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_k","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state k","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_l","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state l","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_m","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state m","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_n","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state n","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_o","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state o","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_p","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state p","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_q","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state q","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_r","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state r","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_s","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state s","reference":"GL1X structural alphabet (internal/fold/gsa.go)"},{"name":"gsa_t","group":"gsa","unit":"fraction","description":"Fraction of residues in GSA state t","reference":"GL1X structural alphabet (internal/fold/gsa.go)"}],"kind":"structure","name":"gl1x-structure-1","prefix":"s_"}],"gl1f":{"default_scale_q":1000,"features_text":"the GL1F NFT features string: one feature name per line, in input order, as a model NFT stores its inputs","note":"a model trained on a dataset's feature columns takes them in the dataset's column order; quantize new inputs with the model's own scale_q","packing":"one little-endian int32 per input in feature order: the bytes the GL1F runtime's predict functions take","quantization":"q = clamp(round(x · scale_q)) to the int32 range, the GL1F Forest input rule (half rounds away from zero for positive x, toward +∞ as JavaScript's Math.round)"},"molnft_paths":{"0xf8a9a5fc2cea6dca15e5e45712a48a33a7bb25fc:3":"/molnft/hla00003-a01030101"},"record":{"accession":null,"collection_name":"MolNFT HLA","contract_address":"0xf8a9a5fc2cea6dca15e5e45712a48a33a7bb25fc","molecular_id":"HLA00003 A*01:03:01:01","molnft_version":"v1","pdb_id":null,"structure_available":true,"title":"HLA00003 A*01:03:01:01","token_id":"3","url":"/molnft/hla00003-a01030101"},"sequences":[],"sequences_truncated":false,"structure":{"chains":[{"accessions":[],"chain_id":"A","chains":["A"],"kind":"protein","notes":["Radius of gyration 35.40 Å, 1.71× that of a compact chain of 365 residues: extended or made of several domains","Secondary structure (TM-align): 29.0% helix in 6 helices, 31.0% strand in 19 strands","1.48 CA contacts per residue, 47.2% long-range; relative contact order 0.102","Mean B-factor 87.6 Ų (sd 9.2)"],"residues":365,"secondary":"CCCCCCCCCCCCCCHCCCCCCCCTCCEEEEEEEEEEEECTCCCCCEEEEEECHTCECCEECCCCTTCCCEECCTHHHCCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCTCCEEEEEEEEEEEECTTCCCCCEEEEEECHTCCCCEECTTCCCEEECCTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCCHHHCCEECCEEEEEEEECCTTCEEEEEEECCCCCCCEEEEEECHTCEECHCCEEECCEECTHTCEEEEEEEEECTHCCHCCEEEEECTCCCTCEEECCCCCCCCCCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEEEEEEECC","set":"gl1x-structure-1","values":[365,35.4017,1.7097,0.4203,130.693,39.093,0.290411,0.309589,0.068493,0.331507,6,19,1.4849,0.306273,0.472325,0.101779,37.1494,0,87.592,9.245,0,0,4.042327,0.084932,0.079452,0.005479,0.073973,0.035616,0.024658,0.052055,0.043836,0.019178,0.10411,0.073973,0.038356,0.027397,0.024658,0.024658,0.027397,0.10411,0.10411,0.030137,0.021918]}],"entry_id":null,"method":null,"predicted":false,"skipped":[],"status":"complete"}}