How to Use PULCHRA Online
Try PULCHRA
Commercially Available Online Web Server
PULCHRA: High-Speed Full-Atom Protein Structure Reconstruction
PULCHRA (Protein Chain Reconstruction Algorithm) is a fast and robust computational method designed to reconstruct full-atom protein models from reduced representations. Developed by researchers at the Burnham Institute for Medical Research and the Georgia Institute of Technology, PULCHRA serves as a critical bridge between coarse-grained protein models and all-atom applications like molecular dynamics, protein-ligand docking, and structure-based function prediction.
By leveraging a hierarchy of structural optimizations, PULCHRA translates approximate protein folds into detailed atomic structures in a fraction of a second, while automatically regularizing distorted geometries to ensure physical plausibility.
Key Innovations: Fast and Flexible Chain Assembly
PULCHRA utilizes a modular reconstruction pipeline that can handle diverse input types, from α-carbon-only traces to side-chain centers of mass.
Multi-Step Reconstruction Pipeline: Features optional, independent steps including α-carbon optimization, backbone reconstruction, side-chain heavy atom placement, and hydrogen addition.
Geometric Regularization: Employs a steepest-descent minimization using a simple harmonic potential to correct unphysical α-carbon virtual bond distances and angles often found in cluster centroids.
Hydrogen Bond Optimization: Adjusts peptide bond orientations to maximize hydrogen bonding patterns in α-helices and β-sheets, using the validated DSSP energy formula.
Advanced Clash Mitigation: Iteratively searches rotamer libraries and rotates side chains around virtual bonds to eliminate over 95% of initial heavy-atom clashes while preserving natural packing.
Physical Plausibility Checks: Automatically detects and attempts to fix "punched" aromatic rings and improper chirality (D-amino acids) that would otherwise break molecular mechanics simulations.
Performance Benchmarks
PULCHRA consistently delivers reconstruction quality comparable to established methods while maintaining a significant advantage in computational speed.
Metric | PULCHRA Result | Key Finding |
Reconstruction Speed | ~0.8s per protein | Up to 36x faster than SCWRL on decoy sets. |
All-Atom RMSD | 0.97 Å | High precision when side-chain centers of mass are provided. |
Backbone Precision | 0.50 Å | Reconstructs backbone atoms with high accuracy from native traces. |
Clash Resolution | > 95% removed | Successfully resolves atomic overlaps even in distorted structures. |
Punched Ring Fixing | ~99% success rate | Outperforms SCWRL and SCATD in generating physically valid decoys. |
Scientific Breakthroughs in Model Building
Bridge Coarse-Grained and All-Atom Space
Reduced protein representations are essential for efficient conformational sampling. PULCHRA allows researchers to perform large-scale folding simulations and immediately convert the resulting ensembles into all-atom formats required for functional analysis or virtual ligand screening.
Robustness Against Distorted Data
PULCHRA was specifically designed to handle "real-world" predicted decoys that often exhibit serious geometric irregularities. In tests on 500 TASSER-generated decoys, it generated reasonable models even where traditional tools failed or produced non-physical arrangement errors like punched rings.
Repertoire and Trajectory Processing
The standalone executable is optimized for high-throughput tasks, including the processing of multi-model PDB files from molecular simulation trajectories and multi-chain quaternary structures.
PULCHRA on Tamarind Bio: High-Throughput Refinement
Tamarind Bio provides a managed, high-performance environment to deploy PULCHRA's reconstruction workflows, removing the need for local compilation or manual PDB manipulation.
No-Code Trajectory Analysis: Automatically process thousands of simulation snapshots to generate all-atom trajectories in minutes.
Scalable Model Refinement: Use PULCHRA as a fast preprocessing step before launching expensive molecular mechanics or docking campaigns on Tamarind’s secure cloud.
How to Use PULCHRA on Tamarind Bio
Access the Platform: Log in to tamarind.bio and select the PULCHRA Reconstruction tool.
Upload Structure: Provide a PDB file containing a reduced protein representation (e.g., α-carbon trace or side-chain centers).
Configure Optimization: Choose to enable or disable specific routines like α-carbon regularization or backbone hydrogen bond optimization.
Set Modeling Modes: Define treatment for multi-chain models, cis-prolines, or known chain breaks.
Run Reconstruction: The platform executes the C-based algorithm to produce full-atom PDB files in milliseconds per structure.
Evaluate Results: Analyze per-residue RMSD reports and DSSP hydrogen bond energy changes before exporting for downstream docking or dynamics.