Reference

RESTful API Reference

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Package Method API Reference

Base, Compounds, PDB, SIFTS

from pdb_profiling.processors import Base, Compounds, PDB, SIFTS

PDBAssembly, PDBInterface

from pdb_profiling.processors import PDBAssembly, PDBInterface

PDBs, SIFTSs

from pdb_profiling.processors import PDBs, SIFTSs

Identifier, Identifiers

from pdb_profiling.processors import Identifier, Identifiers

PDBeModelServer, PDBeCoordinateServer, PDBArchive, PDBVersioned

from pdb_profiling.processors import PDBeModelServer, PDBeCoordinateServer, PDBArchive, PDBVersioned

UniProts, UniProtFASTA, ProteinsAPI, EnsemblAPI, EutilsAPI, SMR

from pdb_profiling.processors import UniProts, UniProtFASTA, ProteinsAPI, EnsemblAPI, EutilsAPI, SMR

Interactome3D

from pdb_profiling.processors.i3d.api import Interactome3D

cif_gz_stream

from pdb_profiling import cif_gz_stream

PISAErrorWarning

from pdb_profiling.warnings import PISAErrorWarning

Column Name Reference

Terminology in PDB

Defined by PDBe

  • pdb_id: PDB Entry ID
  • resolution: (pdb-101-explanation)
  • experimental_method_class: (pdb-101-explanation)
  • experimental_method: x-ray, nmr, em, other
  • revision_date: as name said
  • deposition_date: as name said
  • entity_id: the entity identifier of a PDB Entity; for what is PDB Entity? please look at this link
  • molecule_type
    • polypeptide(L)
      • cyclic-pseudo-peptide
        • e.g. 3q9h,6iqg BUT polypeptide(L) was asigned to entity_poly.type
    • polypeptide(D)
      • e.g.3ue7, struct_asym_id: A
    • polydeoxyribonucleotide
    • polyribonucleotide
    • polydeoxyribonucleotide/polyribonucleotide hybrid
      • e.g. 6ozg
    • carbohydrate_polymer
      • e.g. 2wmg
    • bound
      • ligand
      • sugar
      • other
    • water
  • sequence: one-letter-code of SEQRES
  • pdb_sequence: SEQRES sequence that use one-letter-code for standard amino-acid or nucleotide, three-letter-code-with-brackets for non-standard amino-acid or non-standard nucleotide or UNK
  • ca_p_only: whether the PDB Entity only contains C-alpha atom for each observed residue
  • chain_id: the chain identifier of a PDB Chain defined by author (highly possible to clash among different entity)
    • chain_id: implement by PDBe REST API
    • auth_asym_id: implement by PDBe ModelServer API
    • authAsymId: implement by PDBe CoordinateServer API
  • struct_asym_id: the chain identifier of a PDB Chain (unique across all PDB Entity)
    • struct_asym_id: implement by PDBe REST API
    • label_asym_id: implement by PDBe ModelServer API
    • asymId: implement by PDBe CoordinateServer API
  • residue_number: residue index in the aspect of the PDB Chain’s Sequence (SEQRES, Index from 1)
  • author_residue_number: residue index in the aspect of the PDB Chain’s Sequence but assigned by the author of this PDB Entry
  • author_insertion_code: residue insertion code provided by author in the PDB file
  • multiple_conformers: those alternate conformers modelled for this residue
  • assembly_id
    • 0 stands for asymmetric unit
    • 1 stands for biological assembly 1
    • 2 stands for biological assembly 2
    • and so on
    • for what is asymmetric unit & biological assembly? please click the link
  • interface_id
    • Defined by PISA
    • The interface identifier in the corresponding biological assembly
  • UniProt: UniProt Isoform ID
    • isoform suffix not shown for canonical sequence
  • is_canonical: whether the UniProt Isoform is the canonical isoform defined by UniProt-KB
  • unp_residue_number: residue index in the aspect of the UniProt Isoform’s Sequence (Index from 1)
  • identity: provided by SIFTS: sequence identity of PDB Entity SEQRES with UniProt Isoform (0-1)
  • pdb_start: The starting index of the SIFTS alignment segment in PDB entity SEQRES (Index from 1)
  • pdb_end: The ending index of the SIFTS alignment segment in PDB entity SEQRES (Index from 1)
  • unp_start: The starting index of the SIFTS alignment segment in UniProt Isoform Sequence
  • unp_end: The starting index of the SIFTS alignment segment in UniProt Isoform Sequence

Defined by pdb-profiling

  • multi_method: whether the PDB entry was determined by multiple method

  • 1/resolution: as name said

  • id_score

    • calculated by -sum(ord(i) for i in chain_id)
    • used for multi-criteria sorting of chains according to their chain_id

  • SEQRES_COUNT: the count of the residues in SEQRES

  • OBS_INDEX: the index of observed/modelled (with coordinates) residues of the PDB Chain Instance

  • OBS_COUNT: the count of observed/modelled (with coordinates) residues of the PDB Chain Instance

  • OBS_RATIO_SUM: the sum of the observed/modelled (with coordinates) residues’s ratio of the PDB Chain Instance

  • BINDING_LIGAND_INDEX: the residues that binding to ligands(including carbohydrate polymer) of the PDB Chain Instance

  • BINDING_LIGAND_COUNT: the count of residues that binding to ligands(including carbohydrate polymer) of the PDB Chain Instance

  • STD_INDEX: the index of the standard residues of the PDB Entity

  • STD_COUNT: the count of the standard residues of the PDB Entity

  • OBS_STD_INDEX: the index of the standard residues of the PDB Entity

  • OBS_STD_COUNT: the count of the observed standard residues of the PDB Chain Instance

  • NON_INDEX: the index of non-standard residues of the PDB Entity (including UNK)

  • NON_COUNT: the count of non-standard residues of the PDB Entity (including UNK)

  • UNK_INDEX: the index of the UNK residues of the PDB Entity

  • UNK_COUNT: the count of the UNK residues of the PDB Entity

  • dNTP_INDEX: the index (in SEQRES) of DA|DT|DC|DG|DI in that PDB Entity

  • dNTP_COUNT: the count of DA|DT|DC|DG|DI in that PDB Entity

  • NTP_INDEX: the index (in SEQRES) of A|U|C|G|I in that PDB Entity

  • NTP_COUNT: the count of A|U|C|G|I in that PDB Entity

  • ARTIFACT_INDEX

    • the index of those artifact residues in the PDB Entity
    • including:
      • Cloning artifact
      • Expression tag
      • Initiating methionine
      • Linker

  • Entry: UniProt Entry ID/Accession

  • unp_range: mapped range of the UniProt Isoform’s Sequence with its corresponding PDB Chain’s Sequence (Index from 1)

    • generated from unp_start and unp_end

  • pdb_range: mapped range of the PDB Chain’s Sequence Sequence with its corresponding UniProt Isoform’s (Index from 1)

    • generated from pdb_start and pdb_end

  • new_unp_range: fixed(deal with InDel) mapped range of the UniProt Isoform’s Sequence with its corresponding PDB Chain’s Sequence (Index from 1)

  • new_pdb_range: fixed(deal with InDel) mapped range of the PDB Chain’s Sequence Sequence with its corresponding UniProt Isoform’s (Index from 1)

  • sifts_range_tag

    • (example)
    • Safe
    • Insertion
    • Deletion
    • InDel

  • reversed

    • whether there is reversed mapped range in the aspect of UniProt Isoform Sequence (P00441 5j0c A)
    • SIFTS是以PDB Chain Sequence的视角来匹配序列片段，少数情况会有把部分unp序列反向匹配
    • “5j0c - it the circular permutant structure where authors have swapped the few chunk protein from front and back -(figure 2 in https://pubs.acs.org/doi/pdf/10.1021/jacs.6b05151). That’s why you see “the head of the UniProt sequence is mapped with the tail of the PDB-Chain sequence” – from Preeti Choudhary

  • repeated

    • whether there is repeated mapped range in the aspect of UniProt Isoform Sequence (i.e. Q7KZ85-3 6gmh M)
    • “In SIFTS, the segment generation is done from PDB point of view, that’s why you will see continuous pdb ranges. Seldom, in protein structures, you may see a same protein (uniprot accession) is present in copies/or is repeated” – from Preeti Choudhary

  • conflict_pdb_index: the index(dictionary) of those residues that confilct with the reference sequence(UniProt Isoform) in the pdb mapped range

  • conflict_pdb_range: the range of those residues that confilct with the reference sequence(UniProt Isoform) in the pdb mapped range

  • conflict_unp_range: the range of those residues that confilct with the reference sequence(UniProt Isoform) in the unp mapped range

  • unp_len: the length of the UniProt Isoform Sequence

  • InDel_sum: SEQRES residues that fall into the range of Insertion or Deletion or InDel of the PDB Chain Instance

  • select_tag: whether in the recommanded representative set

  • select_rank: the rank among all the candidate chains for the UniProt Isoform (1st denoted as the best)

  • RAW_BS: the weighted score that measure the correspondence between the UniProt Isoform and the PDB chain instance (apo-state) in the sequence level defined by pdb-profiling

  • RAW_BS_IG3: set the weight of the binding ligand residues to zero and then calculate the RAW_BS

  • _1: denoted as the partner chain 1

  • _2: denoted as the partner chain 2

  • model_id: the model ID of the chain in the corresponding biological assembly PDB format file

    • 0 denoted as the first model

  • asym_id_rank

    • This column is defined in response to replication and rotation operation in the biological assembly
    • It is the index of the order of occurrence of that struct_asym_id in the corresponding biological assembly
    • Both of the name and the content of this column defined by pdb-profiling

  • struct_asym_id_in_assembly

    • This column is defined in response to replication and rotation operation in the biological assembly
    • It is the regenerated struct_asym_id of the chain instance in the corresponding biological assembly
    • For asymmetric unit, the content in this column is the same as the content in the struct_asym_id column
    • The name of this column defined by pdb-profiling
    • The content of this column defined by PDBe

  • unp_range_DSC: the Dice Similarity Coefficient of new_unp_range_1 & new_unp_range_2

  • interface_range_1: the range of the interaction’s interface in the aspect of partner1 chain (Index from 1)

  • interface_range_2: the range of the interaction’s interface in the aspect of partner2 chain (Index from 1)

  • unp_interface_range_1: the range of the interaction’s interface in the aspect of partner1 chain (mapped to the UniProt Isoforom)

  • unp_interface_range_2: the range of the interaction’s interface in the aspect of partner2 chain (mapped to the UniProt Isoforom)

  • i_select_tag: whether in the recommanded interaction representative set

  • i_select_rank: the rank among all the interacting-chains (1st denoted as the best)

  • i_group: the Interaction Group

  • in_i3d: judge whether the PPI is in the interaction3d dataset (condisider both of the UniProt entry interaction and the PDB chain interaction wtih corresponding biological assembly and model-id)

Last updated on Apr 29, 2021