timodonnell / manuscript_ab_epitope_interaction

Welcome!

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Read the manuscript here

• datasets contains:

  • NR_LH_Protein_Martin A dataset of non-redundant ab-ag complexes from AbDb
  • 3did A dataset of protein-protein interactions from 3did

• src contains codes (in Python and R) for main and supplementary figures

• figures contains main and supplementary figures

• dl contains codes for deep learning

• sl contains codes for shallow learning

• suplemental_text contains codes and tex files the derivation of an analytical solution for the theoretical number of motifs within one CDR/FR region

• ramachandran_files contains codes and figures for Ramachandran angle calculations

• Analyses were primarily done using the files:

  • respairs_segment_notationx* (AbDB)
  • threedid_no_iglike_notationx* (3did)

• Raw deep learning models and outputfiles are also available at https://archive.sigma2.no under DOI 10.11582/2020.00060

• Dataset details

Dataset title: Structural interaction motifs data files.

Date: 2019 greifflab.org

preprocessed

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1. File name:

      respairs_segment_notationx_len_merged.csv
   

This file contains residues pairs annotated by region (segment). Along with the structural interaction motifs for paratopes and epitopes.

      Attributes:
          pdbid: a unique identifier of an entry in Protein Data Bank (PDB).
          abchain: antibody chains (light [L] and heavy [H]).
          segment: antibody regions [FR1–3 and CDR1–3] with chain annotations. Follows the Martin numbering scheme.
          paratope: interacting residues in a paratope.
          plen: the number of residues in a paratope.
          shiftset: a set containing the residue number differences in a paratope. 
          gapset: a set containing the number of non-interacting residues (gaps) in a paratope.
          abresnumiset: a set containing the residue number in a paratope.
          ab_motif: structural interaction motif of a paratope.
          absegment: as in `segment`, without chain annotations.
          gapstatus: gap status (0 or 1).
          gapstrstatus: gap status in string (continuous or discontinuos).
          ab_motiflen: the length of structural interaction motif (paratope)
          ag_motiflen: the length of strctural interaction motif (epitope)
          epitope: interacting residues in an epitope.
          epitope_len: the number of residues in an epitope.
          ag_motif: structural interaction motif of an epitope.
          agresnumiset: a set containing the residue number in a paratope. 
          agchain: the chain of the antigen

2. File formats: comma separated file (CSV).
3. Versioning: All changes to this dataset may be documented in a changelog in this README document.
4. A number of files in this directory were derived from this file.

dl/dataset

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1. File name:

      motif*.tsv
      motif*pos*.tsv
      paraepi.tsv
      epipara.tsv
   

These files contain ~5000 pairs of paratope-epitope structural interaction motifs (motif*.tsv) [pos is with position] or pairs of paratope-epitope sequences (paraepi.tsv and epipara.tsv)

      Attributes:
          epipara.tsv: first and second columns are epitope and paratope sequences respectively.
          paraepi.tsv: first and second columns are paratope and epitope sequences respectively.
          motif_epiparadash.tsv: first and second columns are epitope and paratope interaction motifs respectively.
          motif_paraepidash.tsv: first and second columns are paratope and epitope interaction motifs respectively.
          motif_epiparadash_pos.tsv: first and second columns are epitope and paratope interaction motifs respectively. With position annotation.
          motif_paraepidash_pos.tsv: first and second columns are paratope and epitope interaction motifs respectively. With position annotation.

2. File formats: tab separated file (TSV).
3. Versioning: All changes to this dataset may be documented in a changelog in this README document.

dl/dataset_ppi

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1. File name:

      motif*.tsv
      motif*pos*.tsv
      paraepi.tsv
      epipara.tsv
   

These files contain ~20000 pairs of paratope-epitope structural interaction motifs (motif*.tsv) [pos is with position] or pairs of paratope-epitope sequences (paraepi.tsv and epipara.tsv). For protein-protein interaction (PPI), a motif and its interacting partner are the analog to paratope and epitope in antibody-antigen scenario.

      Attributes:
          epipara.tsv: first and second columns are epitope and paratope sequences respectively.
          paraepi.tsv: first and second columns are paratope and epitope sequences respectively.
          motif_epiparadash.tsv: first and second columns are epitope and paratope interaction motifs respectively.
          motif_paraepidash.tsv: first and second columns are paratope and epitope interaction motifs respectively.
          motif_epiparadash_pos.tsv: first and second columns are epitope and paratope interaction motifs respectively. With position annotation.
          motif_paraepidash_pos.tsv: first and second columns are paratope and epitope interaction motifs respectively. With position annotation.

2. File formats: tab separated file (TSV).
3. Versioning: All changes to this dataset may be documented in a changelog in this README document.

NR_LH_Protein_Martin

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1. File name:

      *.pdb
   

These files contain atomic coordinates (atoms and residues) of an antibody-antigen complex in PDB format. Go to PDB format specification.

      Attributes:

2. File formats: protein data bank (PDB).
3. Versioning: All changes to this dataset may be documented in a changelog in this README document.

3did

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1. File name:

      3did_flat.txt
   

The file contains residues pairs (protein-protein interaction, PPI) of all protein complex in pdb pdb version 2019_01. Go to 3did file specification.

      Attributes:

2. File formats: 3did flat file.
3. Versioning: All changes to this dataset may be documented in a changelog in this README document.

2020 GreiffLab