faltwerk 0.5

Spatial analysis of protein structures

Faltwerk

faltwerk is a library for spatial exploratory data analysis of protein structures. It helps parse them, select items of interest, generate and visualise various protein annotations, and then provide convenient interfaces for downstream tools to run, for example, spatial regression. The most convenient way to run faltwerk is in a jupyter notebook. This REPL-like execution gives rapid feedback and can help form hypotheses. However, faltwerk also integrates nicely into workflows (no point and click required).

The curious thing about proteins is that they come as linear strings of residues, but then fold up into 3D structures, that represent the functionally active form of the molecule (the thing that "does stuff"). Correspondingly, nature most often selects on structure. However, many analyses (positive selection etc.) require the linear sequence. faltwerk bridges this gap (see specific use cases below).

PRs and suggestions welcome! The awesome Anvio has a structure module, should you be dissatisfied with faltwerk.

Usage

# TL;DR: Quickly visualize a zinc-finger and annotate the zinc-binding residues

# wget 'http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1MEY' -O 1mey.pdb
from faltwerk import Fold, Binding, Layout

model = Fold('1mey.pdb')
hmms = 'path/to/pfam_v31/Pfam-A.hmm'
b = Binding(model, option='confident')
b.predict_binding_(hmms)  # inplace operation
model.annotate_('binding', b.get_binding('PF13912.5', 'ZN'))
Layout(model).geom_surface('binding').render()

We assume that all protein structures contain a single structure, and if you are not analysing protein complexes, then you want the structures to only contain a single chain, also. A simple way to clean a query pdb file is through pdb-tools (http://www.bonvinlab.org/pdb-tools/). AlphaFold2 predictions as generated by ColabFold are ideal.

More information can be found in the documentation. Additionally, we cover several use cases with jupyter notebooks:

jupyter notebook examples/example_local.ipynb

But let's step through a real world example of the amazing assymetric selection that can be observed in human transferrin as a consequence of bacterial iron piracy, arr!

# Load data
from faltwerk.models import Fold, AlphaFold
# ... (for details see notebook)

fp = 'data/alphafold2/transferrin/test_08df6_unrelaxed_rank_1_model_3.pdb'
model = Fold(fp)

# or
fp = 'data/alphafold2/transferrin/'
af = AlphaFold(fp)
model = af.best

# Visualise pLDDT (how good is AF2 the prediction)
ly = Layout(model).geom_ribbon('plddt', palette='rainbow_r')

# Predict ligand binding sites using the "InteracDome" approach
b = Binding(model, 'representable')
b.predict_binding_(pfam)
binding = b.get_binding('PF00405.16', 'FE')
fe = [i for i, j in enumerate(binding) if j > .5]

ly = Layout(model)
# select
fe_ = ly.select(residues=fe)
# style
ly.geom_ribbon(color='#ffffff')
ly.geom_ribbon(selection=fe_, color='red')
ly.render().show()

# Test for spatial signal in residues that are e. g. mutated or under positive
# natural selection. Here we use residues from Barber et al., Science, 2014
# (https://www.science.org/doi/10.1126/science.1259329) that are under positive
# selection.
original = [153, 253, 382, 434, 435, 436, 439, 558, 574, 575, 576, 591, 592, 593, 614, 617, 619, 625]

# -1 bc/ positions from manuscript are 1-based 
barber2014 = [i-1 for i in original]
selection = [1 if i in barber2014 else 0 for i in range(len(model))]

# (1) Spatial autocorrelation, i. e. "hotspots" in selected features, here using
# the Getis-Ord metric.
FDR = 0.05
hotspots = find_hotspots(
    model,
    selection,
    method='getis_ord',
    angstrom=8,
    false_discovery_rate=FDR,
    test_two_sided=False)

# (2) Point density analysis, here using HDBSCAN.
clusters = cluster(model, hotspots, min_cluster_size=5)

# Annotate model
model.annotate_many_({
    'selection': selection,
    'hotspots': hotspots,
    'clusters': clusters})

# Build figure like a layer cake
ly = Layout(model, panel_size=(200, 200), grid=(1, 3), linked=True)

pos = ly.select(residues=barber2014, elements=['CA'], chain='A')

ly.geom_ribbon(color='#ffffff')
ly.geom_sphere(selection=pos, color='black')
ly.geom_surface('hotspots', palette='binary', panel=(0, 1))
ly.geom_surface('clusters', palette='Set2_r', panel=(0, 2))
ly.render().show()

From here, faltwerk allows to easily interact with downstream tools like altair for visualisation of features or pysal for spatial regression (see notebook example.ipynb)

df = pd.DataFrame.from_dict(
    flatten(model.annotation, expected_track_length=len(model)))

Use cases

• Annotate solvent access, active centers and more
• Some regions in the amino acid sequence are more conserved than others across species. Which regions in the 3D structure do they correspond to?
• Are there any significant spatial hotspots where residues experience positive selection?
• Do observed mutations cluster in any part of the protein, for example in regions that interface other proteins (protein binding sites) or active sites of the protein?
• A hotspot/ cluster has been identified; which protein features if any can explain this occurance. For example, is the cluster associated with known protein-binding sites?
• What's the spatial relationship between mutations deemed pathogenic and the annotated functional domains of a protein?

Install

If you want to programmatically search for hotspots, the easiest way to get started is to use the image we provide through docker:

docker pull nanozoo/faltwerk:3.8--08dc798

Quick start using the colab notebook.

# Dependencies
!pip install faltwerk==0.3
# Install tools from upstream and downstream tasks
!pip install -q pdb-tools altair vega_datasets spreg geopandas
# More dependencies
!mamba install -q -y -c conda-forge -c bioconda foldseek=3.915ef7d hmmer

# For local execution in a jupyter notebook
pip install notebook
jupyter notebook examples/example_local.ipynb

It might be necessary to install a jupyter extension to visualize the proteins (you notice if they don't render). Please refer to the py3Dmol install documentation and repo in this case. A typical setup that renders correctly looks like this (Linux and Mac tested):

# ubuntu 20.04. LTS
# Python 3.10.4

node --version
# v10.19.0

jupyter --version
# IPython          : 8.4.0
# ipykernel        : 6.15.1
# ipywidgets       : not installed
# jupyter_client   : 7.3.4
# jupyter_core     : 4.11.1
# jupyter_server   : not installed
# jupyterlab       : not installed
# nbclient         : 0.6.6
# nbconvert        : 6.5.3
# nbformat         : 5.4.0
# notebook         : 6.4.12
# qtconsole        : not installed
# traitlets        : 5.3.0