bio-substructure-search

Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

Jump to install Review files

Repository: GPTomics/bioSkills
Last source activity: July 15, 2026 at 00:46
Detected SKILL.md language: English
Stars: 1,235
Forks: 274

Install options

The review-first prompt is selected by default. You can switch to a direct command or download a local copy.

Install with an AI assistant

Copy this prompt into the AI assistant you're using.

Follow https://skillsmp.com/skill-install/prompt.md to install only the Agent Skill at https://github.com/GPTomics/bioSkills/tree/main/chemoinformatics/substructure-search.

A direct command skips the review prompt. Inspect the source before running it.

npx skills add https://github.com/GPTomics/bioSkills --skill bio-substructure-search

The command stays on one line. Scroll horizontally to inspect it before copying.

Prefer a local copy? Download the files currently available to SkillsMP.

Review the source files

Read SKILL.md and any companion files shown by SkillsMP before deciding whether to install.

File Explorer

3 files

SKILL.md

Source instructions · Read-only preview

name	bio-substructure-search
description	Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

Back to search Back to installation

clawhub-installer

Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

2026-08-11

bio-seq-objects

Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, building annotated records for file output, or debugging post-1.78 Bio.Alphabet and immutability errors.

2026-08-11

bio-transcription-translation

Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and six-frame ORF finding. Use when converting a CDS or ORF to its amino-acid sequence, selecting a non-standard (mitochondrial, bacterial, ciliate) genetic code, validating a coding sequence, or scanning all reading frames.

2026-08-11

View all from this repository

bio-substructure-search

Source facts

Install options

Install with an AI assistant

Review the source files

More from this repository

Install with an AI assistant

More from this repository