Conformer Generator
Generate conformers for small molecules and ligands using RDkit.
This program is designed for the generation, optimization, and analysis of molecular conformers using the RDKit library. The primary goal is to identify the most energetically favorable and structurally unique conformers of a given molecule through a multi-step process.
Estimated resource cost: 0.0005786150000000001
Categories: Ligand/Drug Design & Screening
Tags: Conformation Generation Free Energy / Binding Energy Small Molecules
Key Capabilities
- First generates a set number of 3D conformers for the input molecule using the ETKDGv3 method, which is known for producing chemically plausible conformations.
- After generating the conformers, the program minimizes the energy of each conformer using a chosen force field method (MMFF94, UFF, or MMFF94s).
- Conformers with energies above a specified threshold (relative to the lowest energy conformer) are filtered out, retaining only the most stable conformers.
- An RMSD (Root Mean Square Deviation) matrix is calculated to measure the structural differences between conformers.
- The program clusters the conformers using the Butina clustering method, which groups conformers based on their RMSD values using a dynamic threshold that considers the molecule's size.
- Within each cluster, the program identifies the conformer with the lowest energy, selecting it as the representative of that cluster.
- The result is a set of unique conformers that represent the most stable structures across the entire conformer set.
Runtime Statistics
| Metric | Value |
|---|---|
| runtime_mean | 368 |
| runtime_median | 20 |
| runtime_std | 3506 |
| runtime_90th_percentile | 115 |
| runtime_max | 60317 |
Similar Tools
- ChemBounce
- Free Wilson Analysis
- GenMol
- PocketFlow
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job. Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: 0.0005786150000000001
Invite-only, limited-time access. Please contact ztang@getantibody.com.
Invite-only, limited-time access. Please contact ztang@getantibody.com.