{"feature_sets":[{"about":"Physico-chemical properties of a protein sequence (ProtParam-compatible) and its composition","features":[{"name":"length","group":"size","unit":"residues","description":"Number of residues"},{"name":"molecular_weight","group":"size","unit":"Da","description":"Average molecular weight (average residue masses plus one water)","reference":"Gasteiger et al. (2005) Protein identification and analysis tools on the ExPASy server"},{"name":"isoelectric_point","group":"charge","unit":"pH","description":"Theoretical pI: the pH at which the net charge is zero (Bjellqvist pK values with terminal-dependent values)","reference":"Bjellqvist et al. (1993) Electrophoresis 14:1023; (1994) 15:529"},{"name":"net_charge_ph7","group":"charge","unit":"e","description":"Net charge at pH 7.0 with the same pK values","reference":"Henderson–Hasselbalch"},{"name":"charge_density_ph7","group":"charge","unit":"e/residue","description":"Net charge at pH 7.0 per residue"},{"name":"extinction_280_reduced","group":"optics","unit":"M^-1 cm^-1","description":"Molar extinction coefficient at 280 nm with every cysteine reduced: 5500·W + 1490·Y","reference":"Pace et al. (1995) Protein Sci 4:2411"},{"name":"extinction_280_cystines","group":"optics","unit":"M^-1 cm^-1","description":"Molar extinction coefficient at 280 nm with every cysteine pair forming a cystine: + 125 per cystine","reference":"Pace et al. (1995) Protein Sci 4:2411"},{"name":"absorbance_280_1mgml","group":"optics","unit":"AU","description":"Absorbance at 280 nm of a 1 mg/mL solution (1 cm, cysteines reduced)"},{"name":"instability_index","group":"stability","description":"Instability index; above 40 suggests a protein unstable in vitro","reference":"Guruprasad et al. (1990) Protein Eng 4:155"},{"name":"aliphatic_index","group":"stability","description":"Relative volume of aliphatic side chains: X(Ala) + 2.9·X(Val) + 3.9·(X(Ile) + X(Leu)), mole percent","reference":"Ikai (1980) J Biochem 88:1895"},{"name":"gravy","group":"hydropathy","description":"Grand average of hydropathy (Kyte–Doolittle)","reference":"Kyte & Doolittle (1982) J Mol Biol 157:105"},{"name":"aromaticity","group":"hydropathy","unit":"fraction","description":"Fraction of F, W and Y","reference":"Lobry & Gautier (1994) Nucleic Acids Res 22:3174"},{"name":"frac_tiny","group":"classes","unit":"fraction","description":"Fraction of tiny residues (ACGST)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_small","group":"classes","unit":"fraction","description":"Fraction of small residues (ABCDGNPSTV)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_aliphatic","group":"classes","unit":"fraction","description":"Fraction of aliphatic residues (AILV)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_aromatic","group":"classes","unit":"fraction","description":"Fraction of aromatic residues (FHWY)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_nonpolar","group":"classes","unit":"fraction","description":"Fraction of nonpolar residues (ACFGILMPVWY)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_polar","group":"classes","unit":"fraction","description":"Fraction of polar residues (DEHKNQRSTZ)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_charged","group":"classes","unit":"fraction","description":"Fraction of charged residues (BDEHKRZ)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_basic","group":"classes","unit":"fraction","description":"Fraction of basic residues (HKR)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"frac_acidic","group":"classes","unit":"fraction","description":"Fraction of acidic residues (BDEZ)","reference":"EMBOSS pepstats residue classes (Rice et al. 2000)"},{"name":"cysteine_count","group":"composition","unit":"residues","description":"Number of cysteines (disulfide capacity)"},{"name":"entropy_bits","group":"complexity","unit":"bits","description":"Shannon entropy of the amino-acid composition"},{"name":"entropy_normalized","group":"complexity","unit":"fraction","description":"Shannon entropy divided by its maximum, log2(20)"},{"name":"low_complexity_fraction","group":"complexity","unit":"fraction","description":"Fraction of residues SEG masks as low complexity (window 12, 2.2, 2.5, as BLAST)","reference":"Wootton & Federhen (1993) Comput Chem 17:149"},{"name":"ambiguous_fraction","group":"complexity","unit":"fraction","description":"Fraction of letters outside the 20 standard amino acids (X, B, Z, J, U, O)"},{"name":"aa_A","group":"composition","unit":"fraction","description":"Fraction of alanine"},{"name":"aa_C","group":"composition","unit":"fraction","description":"Fraction of cysteine"},{"name":"aa_D","group":"composition","unit":"fraction","description":"Fraction of aspartate"},{"name":"aa_E","group":"composition","unit":"fraction","description":"Fraction of glutamate"},{"name":"aa_F","group":"composition","unit":"fraction","description":"Fraction of phenylalanine"},{"name":"aa_G","group":"composition","unit":"fraction","description":"Fraction of glycine"},{"name":"aa_H","group":"composition","unit":"fraction","description":"Fraction of histidine"},{"name":"aa_I","group":"composition","unit":"fraction","description":"Fraction of isoleucine"},{"name":"aa_K","group":"composition","unit":"fraction","description":"Fraction of lysine"},{"name":"aa_L","group":"composition","unit":"fraction","description":"Fraction of leucine"},{"name":"aa_M","group":"composition","unit":"fraction","description":"Fraction of methionine"},{"name":"aa_N","group":"composition","unit":"fraction","description":"Fraction of asparagine"},{"name":"aa_P","group":"composition","unit":"fraction","description":"Fraction of proline"},{"name":"aa_Q","group":"composition","unit":"fraction","description":"Fraction of glutamine"},{"name":"aa_R","group":"composition","unit":"fraction","description":"Fraction of arginine"},{"name":"aa_S","group":"composition","unit":"fraction","description":"Fraction of serine"},{"name":"aa_T","group":"composition","unit":"fraction","description":"Fraction of threonine"},{"name":"aa_V","group":"composition","unit":"fraction","description":"Fraction of valine"},{"name":"aa_W","group":"composition","unit":"fraction","description":"Fraction of tryptophan"},{"name":"aa_Y","group":"composition","unit":"fraction","description":"Fraction of tyrosine"}],"kind":"protein","name":"gl1x-protein-1","prefix":"p_"},{"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 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(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":{"0xd58b01f6c18086e5202cdc5d7ad3e41790360102:30":"/molnft/110M"},"record":{"accession":null,"collection_name":"MolNFT v2 / PDB Bank","contract_address":"0xd58b01f6c18086e5202cdc5d7ad3e41790360102","molecular_id":"110M","molnft_version":"v2","pdb_id":"110M","structure_available":true,"title":"SPERM WHALE MYOGLOBIN D122N METHYL ISOCYANIDE AT PH 9.0","token_id":"30","url":"/molnft/110M"},"sequences":[{"ambiguous":0,"chain_id":null,"chains":[],"is_primary":true,"length":154,"notes":["154 residues, 17,330.1 Da (17.3 kDa) average mass","Theoretical pI 9.00; net charge +3.6 at pH 7 (basic)","Extinction at 280 nm: 15,470 M⁻¹cm⁻¹ with every cysteine pair a cystine, 15,470 reduced; A280 of 1 mg/mL ≈ 0.893","Instability index 14.02: classified stable in vitro (below 40)","GRAVY -0.352: hydrophilic on average; aliphatic index 94.5 (higher suggests more thermostable)"],"sequence":"MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG","sequence_key":"primary","sequence_keys":["primary"],"sequence_type":"protein","set":"gl1x-protein-1","sha256":"7068ee572ee196e373d3371a4de05c2675d7d3b806587160e3769dc7093b663f","values":[154,17330.1,9.0042,3.5705,0.023185,15470,15470,0.8927,14.024,94.4805,-0.3519,0.071429,0.253247,0.383117,0.337662,0.149351,0.525974,0.474026,0.357143,0.227273,0.12987,0,3.945877,0.91299,0,0,0.11039,0,0.038961,0.090909,0.038961,0.071429,0.077922,0.058442,0.123377,0.116883,0.019481,0.012987,0.025974,0.032468,0.025974,0.038961,0.032468,0.051948,0.012987,0.019481]}],"sequences_truncated":false,"structure":{"chains":[{"accessions":["P02185"],"chain_id":"A","chains":["A"],"kind":"protein","notes":["Radius of gyration 15.19 Å, 1.02× that of a compact chain of 154 residues: compact","Secondary structure (TM-align): 72.7% helix in 8 helices, 1.3% strand in 0 strands","0.84 CA contacts per residue, 75.4% long-range; relative contact order 0.361","Mean B-factor 15.5 Ų (sd 5.1)"],"residues":154,"secondary":"CCECTHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCHHHHHCCHCCCCCCTHHHHCCCHHHHHHHHHHHHHHHHHHTCTCCCHHHHHHHHHHHHHCCECTHHHHHHHHHHHHHHHHHCCHHCCTHHHHHHHHHHHHHHHHHHHHHHHTTCCC","set":"gl1x-structure-1","values":[154,15.1903,1.0183,0.0898,43.098,21.06,0.727273,0.012987,0.051948,0.207792,8,0,0.8442,0.053846,0.753846,0.361139,55.6154,0,15.471,5.139,0,0,3.258336,0,0.019481,0.012987,0.012987,0.038961,0.194805,0,0.012987,0.025974,0.116883,0.012987,0.019481,0,0.019481,0.025974,0.077922,0.090909,0.006494,0.279221,0.032468]}],"entry_id":"110M","method":"X-RAY DIFFRACTION","predicted":false,"skipped":[],"status":"complete"}}