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molclaw-run-bioemu

Generate BioEmu conformational samples from sequences and extract per-frame PDBs.

28|2|Updated Mar 31, 2026
Search Tags:#pdb#structure-extraction#bioemu#conformational-sampling#ensemble-extraction#sidechain-relaxation#sequence-sampling
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-run-bioemu
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molclaw-run-bioemu
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-run-bioemu
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-run-bioemu

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Enables automated generation of conformational ensembles from sequence inputs using BioEmu and extraction of per-frame structures for downstream conformation analysis, removing manual handling of trajectories and topology files.

Core Features & Use Cases

  • Sequence-driven sampling: Run BioEmu on sequence strings or FASTA/A3M inputs to produce multiple conformational samples.
  • Per-frame structure extraction: Export individual PDBs, merged multi-model PDBs, and ensemble statistics for downstream workflows.
  • Operational controls & validation: Supports dry-run validation, configurable sample counts, optional sidechain relaxation, NPZ extraction, and merged export modes; ideal for ensemble analysis, structure-based modeling, and reproducible benchmarking.

Quick Start

Run BioEmu sampling for sequence GYDPETGTWG with 5 samples and then extract individual PDBs from the produced run directory for local download and verification.

Frequently Asked Questions about molclaw-run-bioemu

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

FAQPage Schema
How do I generate conformational ensembles from a protein sequence?▼

To generate conformational ensembles, you can use sequence-driven sampling by providing sequence strings or FASTA/A3M inputs to produce multiple conformational samples automatically.

How do I extract individual PDB files from BioEmu outputs?▼

You can extract individual PDB files from BioEmu outputs by using per-frame structure extraction, which supports exporting individual PDBs, merged multi-model PDBs, and NPZ extraction.

Can I run sidechain relaxation and dry-run validation during conformational sampling?▼

Yes, conformational sampling supports optional sidechain relaxation for structure refinement and dry-run validation to verify configurations before executing the full sampling workflow.

What is the best way to control sample counts for sequence-based conformational sampling?▼

The best way to control sample counts is through configurable sample counting parameters, allowing you to specify the exact number of conformational samples generated for your sequence inputs.

Do I need to download generated structure files for ensemble analysis?▼

Yes, you need to download all generated structure files for local verification to ensure accurate downstream conformational analysis, ensemble statistics, and structure-based modeling workflows.

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