molclaw-equiscore-tool

Extracts pockets from docking-result SDFs and scores ligand-pocket pairs with EquiScore to CSV predictions.

28|2|Updated Mar 31, 2026
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-equiscore-tool
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: molclaw-equiscore-tool
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-equiscore-tool
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-equiscore-tool

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates the extraction of binding pockets from docking outputs and the scoring/ranking of ligand-pocket pairs so researchers can convert docking results into prioritized candidate lists without manual preprocessing.

Core Features & Use Cases

  • Pocket extraction: Split docking-result SDFs into single-molecule SDFs and generate pocket folders ready for screening.
  • EquiScore screening: Batch GPU-enabled scoring that produces per-pocket CSV predictions and summary statistics for ranking and enrichment-style filtering.
  • End-to-end pipeline: One-click workflow that runs pocket extraction then screening and returns organized run directories, making it suitable for virtual screening, hit prioritization, and downstream validation workflows.

Quick Start

Run the EquiScore pipeline on a docking-result SDF and receptor PDB to obtain a ranked prediction CSV and organized run directory.

Frequently Asked Questions about molclaw-equiscore-tool

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

FAQPage Schema
How do I extract binding pockets from docking outputs for virtual screening?

EquiScore batch screening evaluates ligand-pocket pairs using GPU-enabled inference to produce per-pocket prediction CSVs. It generates summary statistics for ranking, enabling rapid enrichment-style filtering of virtual screening results.

Can I run an end-to-end docking-to-score pipeline in one step?

The end-to-end pipeline runs pocket extraction then EquiScore screening in one click. It returns organized run directories and ranked prediction CSV paths, making it suitable for hit prioritization and downstream validation workflows.

Does the EquiScore pipeline support GPU batch inference for multi-pose evaluation?

EquiScore supports GPU batch inference and multi-pose evaluation to accelerate scoring. It also includes dry-run validation features to verify inputs before executing the full virtual screening ranking process.

How do I convert docking results into prioritized candidate lists without manual preprocessing?

The automated workflow extracts binding pockets from docking outputs and scores ligand-pocket pairs using EquiScore. It produces ranked prediction CSVs from your SDF and PDB inputs, eliminating manual preprocessing for candidate prioritization.