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conformer-generation

separate

Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

When to use

• preparing 3D ligands for docking
• generating descriptor input for 3D QSAR
• sampling macrocycle/peptide conformational ensembles
• multi-conformer docking
• 3D descriptors / pharmacophores
• FEP input preparation
• shape search

When not to use

• docking pose validation
• free-energy methods

Skill page

Source