StaulliQ · Trinity College Dublin · Biochemistry / Biochemical Sciences

Mechanistic stalling analysis for the ribosome exit tunnel.

StaulliQ is a research software platform for sequence-resolved analysis of ribosomal stalling, enhanced Chou–Fasman secondary-structure prediction, AlphaFold/DSSP comparison, chemistry-aware clustering, and batch-scale exploration of co-translational folding.

Get StaulliQ Read instructions Vincent Kelly Lab

±15context-weighted stalling window

3Dstructure-linked visualisation workflow

Batchmulti-sequence screening and export

Part of Trinity College Dublin

Developed in the Vincent Kelly lab within the Trinity biochemistry / biochemical sciences research environment, with focus on queuine-linked translational control and nascent-chain folding.

What StaulliQ does

The platform was built to move beyond simple pause-site detection and instead explain why stalling occurs and how it connects to secondary-structure emergence in the ribosome exit tunnel. It integrates a stalling predictor with an enhanced Chou–Fasman framework and structure comparison tools in one data-driven workflow.

Physicochemical scoring

Quantifies electrostatic charge, hydrophobicity, polarity, aromaticity, proline content, and queuine-linked effects across an upstream tunnel-sized window.

Structure-aware modelling

Maps A-site stalling to α-helix, β-strand, and coil formation at the ribosome exit using a tunable Chou–Fasman implementation.

Mechanistic interpretation

Separates likely causes of slowdown into electrostatic braking, hydrophobic friction, folding checkpoints, and Q-dependent decoding modes.

Research context

StaulliQ is presented here as a research-facing software page for Trinity College Dublin. The site highlights the software identity, interface, and analytical modules while providing a clear route for installation and lab attribution.

Created by

Souvlakias 67

Lab attribution

Vincent Kelly Lab, Trinity College Dublin, The University of Dublin.

Codebase

Python desktop application with GUI-driven workflows for stalling analysis, Chou–Fasman prediction, AlphaFold comparison, CoolPolarity clustering, GROMACS-inspired mechanism scoring, and batch exports.

Python Tkinter GUI Matplotlib Bio.PDB AlphaFold / DSSP comparison

Core software features

The current interface exposes separate analysis paths for single-sequence prediction, optional motif-based pausing input, structural comparison, chemistry-aware clustering, 3D viewing, and batch workflows. The uploaded Python GUI also includes dedicated windows for AlphaFold comparison, CoolPolarity clustering, batch protein inspection, and Gromacs simulations.

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Stalling probability calculation

Computes residue-level stalling probabilities using local A-site features and weighted neighbourhood context, with optional motif-folder support for machine-learning-derived pausing maps.

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Enhanced Chou–Fasman prediction

Predicts α, β, and coil states with tunable windows, thresholds, and support for modified residue propensities under ribosome-constrained conditions.

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Mechanism classification

Decomposes slowdown into electrostatic braking, hydrophobic friction, folding checkpoints, and queuine-dependent decoding hotspots.

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CoolPolarity clustering

Groups high-stalling residues by local chemistry context to identify positive-biased and hydrophobic-enriched environments along the sequence.

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AlphaFold / DSSP comparison

Compares Chou–Fasman-derived structure assignments against uploaded .pdb or .dssp data to highlight agreement, mismatches, and confidence patterns.

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Batch analysis

Processes multiple proteins at once, generates heatmaps and regional summaries, and opens per-protein inspector views for targeted follow-up.

Inside the software

The gallery below is built from the interface and analysis images you provided. It gives visitors a quick visual path through StaulliQ’s major modules, from single-protein scoring to chemistry clustering and batch analytics.

StaulliQ interface using legacy amino-acid stalling table — Main interface with legacy AA-table scoring, sequence input, tunable stalling and Chou–Fasman parameters, and residue-level plots.

StaulliQ interface using MLP motif folder scoring — Optional motif-folder mode for machine-learning-guided pausing workflows, keeping the same integrated visual analysis pipeline.

CoolPolarity clustering of high-stalling residues — CoolPolarity clustering links high-stalling residues to local chemistry context and exposes characteristic polarity signatures across the tunnel window.

StaulliQ AlphaFold and DSSP comparison view — AlphaFold / DSSP comparison panel with overlap statistics, confusion matrix, region metrics, and pLDDT distribution.

Batch analysis summary — Global batch heatmap view comparing protein-wide stalling patterns against secondary structure class and start/middle/end distribution.

Batch analysis detailed inspector — Per-protein batch inspector with sortable tabular metrics and linked visual summaries for deep sequence-level interpretation.

Gromacs-inspired simulations module — Mechanism-aware site finder that scores candidate A-sites and summarizes local electrostatic, hydrophobic, Q, and folding contributions.

How the workflow fits together

StaulliQ is organised as a modular analysis environment so users can move from raw sequence input to interpretation without leaving the interface.

Load inputs

Bring in stalling tables, Chou–Fasman parameter sheets, optional pausing folders, and gene or protein sequences.

Run stalling analysis

Generate per-residue stalling scores using weighted neighbourhood context and optional motif-derived probabilities.

Interpret structure

Overlay Chou–Fasman predictions, compare with AlphaFold/DSSP outputs, and inspect residues emerging at the ribosome exit.

Export & compare

Save CSV/XLSX outputs, screen multiple proteins, inspect top candidate sites, and communicate findings with linked figures.

Download StaulliQ

The current downloadable package contains the example input files and sample pause directory needed to run the software once the .exe is placed into the release bundle.

Included in the current package

Stalling probability.xlsx
amino_tables_Chou_Fasman.xlsx
pause_directory/ with all .txt pausing files
full_gene_list_short.xlsx

Get StaulliQ Open instructions

Release note

The website build already points to the sample package. You can later replace or extend this zip with the final Windows executable and keep the same download button.

Quick start

Open the instructions page for a short guided setup: launch the .exe, load the stalling file and amino-acid table, confirm the default PDIA3 sequence, and press Run analysis.

Default gene: PDIA3 Optional MLP mode Pause directory support CSV / XLSX export AlphaFold comparison

Suggested acknowledgment

StaulliQ software platform developed within the Vincent Kelly lab, Trinity College Dublin, with website presentation prepared for public-facing software description and download distribution.