PULCHRA
Reconstruct all-atom protein structures from C-alpha or reduced protein PDB models.
Overview
PULCHRA, the PowerfUL CHain Restoration Algorithm, rapidly reconstructs all-atom protein models from reduced protein representations such as C-alpha traces. It can rebuild backbone and side-chain atoms, optionally optimize C-alpha geometry, use side-chain center-of-mass records from PDB-SG inputs, and produce structures suitable for visualization or downstream cleanup workflows.
Run PULCHRA on Neurosnap
The PULCHRA online webserver allows anybody with a Neurosnap account to run and access PULCHRA, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Reconstructs full-atom protein models from C-alpha or otherwise reduced PDB representations.
- Can rebuild backbone atoms, side chains, or both depending on the selected reconstruction mode.
- Optionally optimizes C-alpha positions while preserving a configurable maximum coordinate shift.
- Supports PDB-SG side-chain center-of-mass inputs for improved reconstruction when those pseudoatoms are available.
- Provides optional hydrogen output, AMBER-compatible atom ordering, and optimization trajectory export.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access PULCHRA using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using PULCHRA in publications or research outputs.
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Rotkiewicz P, Skolnick J. Fast procedure for reconstruction of full-atom protein models from reduced representations. Journal of Computational Chemistry. 2008;29(9):1460-1465. https://doi.org/10.1002/jcc.20906 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |