conformer-generation
CommunityGenerate 3D conformer ensembles for ligands with RDKit, optimized for docking and QSAR.
Authorpradyumnasagar
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill provides a method for generating 3D conformer ensembles from SMILES strings, suitable for use in molecular docking and 3D QSAR models.
Core Features & Use Cases
- 3D Conformer Generation: Creates conformer ensembles with RDKit and optimizations using force fields.
- Energy Minimization: Optimizes conformers to local energy minima with MMFF94/UFF or CREST + GFN2-xTB.
- Filtering & Pruning: Applies RMSD pruning and energy filtering to the conformer ensembles.
- Use Case: Prepare 3D ligands for molecular docking studies or generate descriptors for QSAR analysis.
Quick Start
Use the conformer-generation skill to generate conformers for the molecule represented by 'CCO' and filter for the top 20 conformers with RMSD < 1.0 Å.
Dependency Matrix
Required Modules
rdkitopenmmxtbcrest
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: conformer-generation Download link: https://github.com/pradyumnasagar/open-research-skills/archive/main.zip#conformer-generation Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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