Use Conformer Generator
Official Neurosnap webserver for accessing Conformer Generator online.
Overview
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.
Neurosnap Overview
The Conformer Generator online webserver allows anybody with a Neurosnap account to run and access Conformer Generator, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.
View PaperFeatures
- 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.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access Conformer Generator using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
Job Note
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Configuration & Options
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