Enumerate clash-free catalytic rotamer assemblies from Rosetta CST files into PDB outputs.
npx skills add https://github.com/LiorZ/protein-design-skills --skill invrotzyme
Please help me install this Agent Skill. Skill: invrotzyme Source: https://github.com/LiorZ/protein-design-skills/tree/main/skills/invrotzyme Command: npx skills add https://github.com/LiorZ/protein-design-skills --skill invrotzyme
Inverse-rotamer assemblies around a Rosetta CST-defined active site are produced to enable rapid, design-ready outputs for downstream enzyme-design pipelines, including RFdiffusionAll-Atom workflows.
Run invrotzyme.py with a CST file and supporting parameter files to generate PDBs ready for RFdiffusionAA.
High-intent search queries and answers about installing and using this skill.
Generating clash-free catalytic rotamers from a Rosetta CST file requires enumerating inverse-rotamer assemblies around the defined active site. This PyRosetta-based CLI consumes CST files and outputs design-ready PDBs with per-assembly REMARK 666 headers.
Yes, inverse-rotamer assemblies can anchor motifs in RFdiffusion All-Atom workflows. The tool outputs PDB files specifically designed for RFdiffusionAA pipelines, supporting motif integration and stub length configuration to tailor scaffolds for downstream diffusion.
A CST file defines the geometric constraints for the enzyme active site, serving as the input for enumerating rotamer assemblies. The script processes these constraints to produce clash-free catalytic rotamer configurations ready for Rosetta enzdes workflows.
Yes, invrotzyme supports per-CST parameter flags and SLURM-aware parallelization. It provides per-CST controls for tailored scaffolds and utilizes SLURM-aware parallelization to manage the computational load of generating multiple design-ready PDB outputs.
Preparing Rosetta enzdes inputs using PyRosetta involves running a single-script tool to enumerate clash-free rotamers. It generates PDB outputs with motif support and stub configuration, satisfying the requirements for downstream Rosetta-based constraints pathways.
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