molclaw-pack-sidechains

What problem does it solve?

Accurately places full-atom protein sidechain conformations on backbone-only PDBs to prepare structures for downstream modeling, docking, or simulation workflows while reducing manual rotamer adjustment and steric clashes.

Core Features & Use Cases

• Predicts full-atom sidechains from backbone PDBs using AttnPacker and returns an output PDB and run directory for verification.
• Supports device selection, chunked inference for long proteins, and optional rotamer post-processing with configurable optimization iterations and steric weights.
• Use cases include preparing receptor structures for virtual screening, initializing systems for molecular dynamics, and generating consistent inputs for comparative binding evaluations.
• Enforces a mandatory output download step to ensure generated structure files are saved locally for reproducibility and verification.

Quick Start

Pack full-atom sidechains for the uploaded backbone file /path/to/input.pdb using device cuda:0 and return the output PDB path.