Trypanosoma brucei predicted protein structures, part 2 of 2

AlphaFold2-predicted protein structures for the Trypanosoma brucei (TREU927) proteome, predicted using  input multiple sequence alignments optimised for the Discoba lineage in which T. brucei sits. The structure prediction methodology was exactly as described in doi:10.1371/journal.pone.0259871.

This deposition contains part 2 of 2. To get the full dataset, also download TbruceiTREU927_part1.zip from doi:10.5281/zenodo.7940748.

Data are organised with one directory per T. brucei TREU927 gene ID (eg. Tb927.1.3600). Within each directory you will find:

<gene id>_predmap.png A left to right representation of the linear protein sequence with one pixel per amino acid. Each horizontal bar represents one structure prediction, colour coded by pLDDT. For small proteins, there will likely be one prediction of the full-length protein. For large proteins, there may be many overlapping predictions.

<gene id>_<start aa>-<end_aa> A directory containing structure prediction of that gene ID between the start and end amino acid. Within this directory you will find:

<gene id>_<start aa>-<end_aa>.json The full data in a JSON format, including linear protein sequence and metadata, along with 5 predicted protein structures ranked from best to worst overall pAE. For each predicted protein structure, the structure (PDB format), its pLDDT per residue and pairwise pAE.

<gene id>_<start aa>-<end_aa>_1.pdb The PDB file of the highest ranked structure.

<gene id>_<start aa>-<end_aa>_1-pae.png A plot of pAE, for the highest ranked structure, at one pixel per amino acid. Shade of green represents pAE for that amino acid pair, see below.

<gene id>_<start aa>-<end_aa>_1-plddt.png A plot of pLDDT, for the highest ranked structure, at one horizontal pixel per amino acid. Bar height and colour both represent pLDDT for that amino acid, see below.

PDB structure and pAE/pLDDT of lower ranked models are embedded in the JSON file.

All pLDDT and pAE plots use the colour scales used by https://alphafold.ebi.ac.uk/: For pLDDT: > 90 (dark blue), 90 > pLDDT > 70 (light blue), 70 > pLDDT > 50 (orange), < 50 (yellow) discontinuous. For pAE: 0 (white angstrom) to dark green (32 angstrom) continuous.

If you use this resource, please cite this Zenodo deposition and doi:10.1371/journal.pone.0259871.