skills.rest
pradyumnasagar
pradyumnasagarCOMMUNITY
Explore all skills by this author →
𝕏@pradyumnasagarGitHub

conformer-generation

Generate 3D conformer ensembles from SMILES with RDKit and force-field optimization.

6|2|Updated Jun 11, 2026
Search Tags:#molecular docking#conformer generation#ligand preparation#3D QSAR#SMILES parsing
One-click install
npx skills add https://github.com/pradyumnasagar/open-research-skills --skill conformer-generation
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: conformer-generation
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/chemoinformatics/conformer-generation
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill conformer-generation

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit, openmm, xtb, crest, and includes scripts (resource) and references (resource) components.

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.

Frequently Asked Questions about conformer-generation

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

FAQPage Schema
How do I generate 3D conformers from SMILES for molecular docking?▼

Generating 3D conformers from SMILES involves parsing the string with RDKit to build an initial ensemble. This Skill automates that process, creating conformer sets optimized for molecular docking and 3D QSAR preparation.

What's the best way to minimize ligand conformer energy using xTB and CREST?▼

Minimizing ligand conformer energy is best achieved by applying CREST with GFN2-xTB optimization. This Skill integrates those tools to optimize conformers to local energy minima beyond standard force fields like MMFF94.

Does conformer generation work with OpenMM and RDKit for ligand preparation?▼

Yes, conformer generation works with OpenMM and RDKit for ligand preparation. This Skill requires both as dependencies to generate 3D conformer ensembles suitable for docking and 3D QSAR studies.

How do I filter and prune conformer ensembles by RMSD and energy?▼

Filtering and pruning conformer ensembles is done by applying RMSD thresholds and energy windows to remove redundant structures. This Skill applies RMSD pruning and energy filtering to refine the generated conformer sets.

When do I need multiple 3D conformers for 3D QSAR analysis?▼

Multiple 3D conformers are needed for 3D QSAR analysis when generating molecular descriptors that depend on spatial flexibility. This Skill creates conformer ensembles to capture structural variance for QSAR models.

Related Skills

jakechen1jakechen1

mol-render

Generate 3D ball-and-stick molecular renderings from SMILES or PDB structures.

Community
Intermediate
shushuznshushuzn
4

rowan

Run cloud molecular modeling and medicinal-chemistry workflows via a Python API client.

Community
Advanced
yf8578yf8578
1

molecular-dynamics

Run molecular dynamics simulations with OpenMM and analyze trajectories using MDAnalysis.

Community
Advanced
xjtulycxjtulyc
33

openbabel-conversion

Convert chemical file formats and generate 3D structures and conformers.

Community
Advanced