A modern, standalone web interface for fluorescent protein simulation that allows users to configure parameters and run simulations through a user-friendly interface. No external dependencies required - fully self-contained deployment.
FPSIMP is a fluorescent protein (FP) simulation pipeline (SIMP) that SIMPlifies the simulations of FPs and puts IMP (Integrative Modeling Platform) and AlphaFold on a leash to simulate fluorescence observables of proteins and protein assemblies, freely diffusing or bound to a membrane.
FPSIMP uses AlphaFold to predict complex structures, identifies fluorescent proteins by sequence similarity, detects linker regions, coarse-grains the molecular assembly in IMP, and samples the accessible conformational space to determine possible distances and orientation factors between FPs. This simulation pipeline helps design experiments for:
- Fluorescent protein tagging of soluble and membrane-bound proteins
- FRET prediction and analysis for fluorescent protein pairs
- Integrative modeling of protein complexes with fluorescent tags
- Distance and orientation measurements between fluorescent proteins
- Membrane-associated protein simulations with fluorescent markers
- AlphaFold Input: Use AlphaFold-predicted structures as input
- Interactive Sequence Display: View sequences with membrane region marking
- Comprehensive Parameter Configuration: All CLI parameters available through web forms
- Job Queue System: Asynchronous job processing with Celery and Redis
- Real-time Status Updates: Live job status monitoring with progress indicators
- Result Download: Download RMF files and other simulation outputs
- Membrane Region Marking: Click and drag to mark membrane-anchored regions
- Docker Deployment: Complete containerized deployment with docker-compose
- Standalone: No external dependencies - fully independent
- Docker and Docker Compose
- Git
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Clone the repository:
git clone https://github.com/fluorescence-tools/fpsimp cd fpsimp -
Start the application:
docker-compose up -d
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Access the application:
- Web Interface: http://localhost:5000
- Celery Monitor: http://localhost:5555
- Upload your AlphaFold-predicted structure file
- The sequence will be displayed for membrane region marking
- Click and drag on the sequence to select membrane-anchored regions
- Selected regions will be highlighted in yellow
- Use "Clear Membrane Regions" to reset selections
The interface provides all fpsim CLI parameters organized into sections:
- pLDDT Rigid Threshold: Confidence threshold for rigid regions (default: 70.0)
- Min Rigid Body Length: Minimum length for rigid segments (default: 12)
- Bead Size: Residues per bead for flexible regions (default: 10)
- Number of Frames: Total simulation frames (default: 100,000)
- Steps per Frame: MC steps per frame (default: 10)
- Barrier Radius: Confinement radius (default: 100.0 Å)
- Reuse Results: Skip completed steps
- Enable Membrane: Add membrane restraints
- Membrane Weight: Restraint strength (default: 10.0)
- Compute Measurements: Calculate FP distances and orientations
- Generate Plots: Create 2D histograms and marginals
- Click "Submit Job" to start the pipeline
- You'll receive a unique Job ID for tracking
- The job progresses through stages: Queued → Running → Sampling Complete → Completed
- Real-time status updates with progress bar
- Status indicators for each pipeline stage
- Error reporting if jobs fail
- Once completed, download RMF files and other outputs
- Results include topology files, segments, and simulation trajectories
The web interface includes a complete, standalone fpsim implementation:
- PipelineConfig: Uses the integrated pipeline module for job execution
- Parameter Mapping: All CLI parameters are supported through the web interface
- AlphaFold Integration: Direct use of AlphaFold-predicted structures
- Membrane Regions: Visual selection translates to membrane_seq parameters
- No External Dependencies: Completely self-contained
This project is licensed under the GNU General Public License v3.0. See the LICENSE file for details.