Welcome to ProLint!¶

ProLint is a Python library for analyzing biomolecular interactions from molecular dynamics simulations. Built on MDAnalysis, it offers great efficiency in contact calculations and trajectory manipulation, proposing a simple four-step workflow: load your simulation, compute contacts between user-defined atom groups, analyze the results, and generate publication-ready plots. In addition, it provides a React-based web dashboard for interactive exploration of interaction results.

Basic Example¶

from prolint import Universe

# Load simulation
universe = Universe("topology.gro", "trajectory.xtc")

# Compute contacts (default: protein vs non-protein)
contacts = universe.compute_contacts(cutoff=7.0)

# Run analysis
result = contacts.analyze("timeseries", database_type="CHOL")

# Visualize
from prolint.plotting import plot
fig, ax = plot("heatmap", result, colorscheme="viridis")
fig.savefig('heatmap.png', dpi=150, bbox_inches="tight")

Tip

By default, ProLint analyzes interactions between protein and non-protein atoms. Customize this by setting universe.query and universe.database to any valid MDAnalysis selection.

Available Analysis Types¶

Analysis	Use when	Plotters
`timeseries`	Track contact counts over trajectory time	`heatmap`, `timeseries`
`metrics`	Compare residues by occupancy, mean, max, or sum	`residue_metrics`, `logo_grid`
`density_map`	Visualize spatial distribution around query	`density_map`
`radial_density`	Measure density as function of distance from query	`radial_density`
`shared_contacts`	Find residues contacting the same molecules	`heatmap`, `network`
`database_contacts`	Track which molecules contact a specific residue	`database_contacts_heatmap`
`distances`	Track distance between residue pairs over time	`distance_timeseries`
`atom_distances`	Get atom-atom distance matrix at a frame	`distance_heatmap`
`kinetics`	Measure binding dynamics and residence times	`survival_curve`, `residence_distribution`, `contact_events`

See the Analysis and Plotting APIs for details.

Web Dashboard¶

For users who prefer a graphical interface, ProLint includes an interactive web dashboard. It allows you to upload simulation files, configure analysis parameters, and explore results, all without writing code. See the Web Dashboard Tutorial for an introduction to its usage.

Citation¶

If ProLint contributes to your research, please cite:

@article{prolint_2024,
  title={ProLint v. 2: An optimized tool for the analysis and visualization of lipid-protein interactions},
  author={Ramirez-Echemendia, Daniel P.; Sejdiu, Besian I.; Tieleman, D. Peter},
  journal={Biophysical Journal},
  year={2024}
}

License¶

ProLint is released under the MIT License.