invrotzyme

Name: invrotzyme
Availability: InStock
Author: LiorZ

Enumerate clash-free catalytic rotamer assemblies from Rosetta CST files into PDB outputs.

2|Updated May 12, 2026

Search Tags:#pdb #rosetta #rf-diffusion #pyrosetta #enzyme-design #inverse-rotamer #cst-file

Ready to run

npx skills add https://github.com/LiorZ/protein-design-skills --skill invrotzyme

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

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.

Core Features & Use Cases

Single-script PyRosetta tool that consumes a CST file and emits PDBs with per-assembly REMARK 666 headers.
Supports motif integration, per-CST controls, and stub length configuration to tailor scaffolds for downstream diffusion or Rosetta enzdes steps.
Outputs are designed for RFdiffusion All-Atom pipelines as well as Rosetta-based constraints pathways.

Quick Start

Run invrotzyme.py with a CST file and supporting parameter files to generate PDBs ready for RFdiffusionAA.

Frequently Asked Questions about invrotzyme

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I generate clash-free catalytic rotamers from a Rosetta CST file for enzyme design?▼

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.

Can I use inverse-rotamer assemblies to anchor motifs in RFdiffusion All-Atom workflows?▼

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.

What is the role of a CST file in enumerating enzyme active-site rotamers?▼

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.

Does invrotzyme support per-CST parameter flags and SLURM-aware parallelization?▼

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.

How do I prepare Rosetta enzdes inputs using PyRosetta and clash-free rotamers?▼

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.