PULCHRA is Now Available on Vecura

What is PULCHRA?

PULCHRA (PowerfUL CHain Restoration Algorithm) is a fast, classical, non-machine-learning algorithm written in ANSI C that reconstructs stereochemically sound, full-atom protein models from reduced coordinate representations—most commonly just the C-alpha (CA) atom positions. It achieves this by querying pre-compiled rotamer and fragment libraries keyed on local CA geometry, all while performing an initial regularization step to ensure geometric validity.

It helps users bridge the gap between coarse-grained simulations, homology models, and downstream all-atom applications. It is especially useful for rapidly generating high-quality starting structures for energy minimization, molecular docking, or visualization after workflows that output only backbone centroids.

What can users do with PULCHRA on Vecura?

With PULCHRA on Vecura, users can:

• Reconstruct complete backbone atoms (N, C, O) and all side-chain heavy atoms from a simple C-alpha-only PDB file.

• Fine-tune reconstruction with optional parameters, such as enabling side-chain center-of-mass input (-g), limiting CA atom shifts during regularization (-u), optimizing backbone hydrogen bonds (-q), or including hydrogen atoms (-h).

• Process multi-chain proteins in a single pass, preserving chain IDs and residue numbering for seamless integration into existing pipelines.

• Generate production-ready, full-atom PDB files in milliseconds per protein, enabling high-throughput structural refinement without external dependencies or file I/O overhead.

What the output means

The output provides a rebuilt full-atom PDB file containing all backbone and side-chain heavy atoms (and hydrogens, if requested).

This output should be used to support scientific decision making. It does not replace experimental validation.

Why this matters

In modern structural biology, many powerful tools—from coarse-grained molecular dynamics to deep learning-based fold predictors—output simplified protein representations. However, most downstream applications (e.g., molecular docking, free-energy calculations, or structure visualization) require full-atom detail. PULCHRA fills this critical gap with unmatched speed and reliability, acting as a deterministic, lightweight, and highly optimized "translation layer" between abstraction and atomic reality. Its integration into Vecura democratizes access to this essential tool, removing the need for local compilation, dependency management, or command-line expertise, thereby accelerating the path from model generation to biological insight.

• Developed by: Burnham Institute for Medical Research and Georgia Institute of Technology

• Source: https://github.com/euplotes/pulchra

• Reference: https://www.tamarind.bio/tools/pulchra