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 Paper

Features

  • 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.

Statistic Value
Credit Usage Rate loading...
Estimated Total Cost loading...
Runtime Mean loading...
Runtime Median loading...
Runtime Standard Deviation loading...
Runtime 90th Percentile loading...
Runtime Longest loading...

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

Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.

Configuration & Options

Service Inputs

The input small molecule you want to create conformers for.

Core Settings

The initial number of random conformers to generate. These conformers will be filtered and the number that will be returned will be less

A minimization step is conducted to minimize free energy to filter out energetically unfavorable conformers. The UFF force field is suitable for a broad range of molecules, including organics, inorganics, and organometallics. It is fast and provides reasonable geometries. MMFF94 is more accurate for organic molecules, especially when dealing with pharmaceuticals. It is recommended for more precise calculations but is slightly slower than UFF. While MMFF94 is already quite accurate, using the "MMFF94s" variant can provide even more accurate energy minimization, particularly for systems that include steric effects like lone pairs or pi-pi interactions. Some experiments and most theoretical calculations show significant pyramidal “puckering” at nitrogens in isolated structures. The MMFF94s (static) variant has slightly different out-of-plane bending and dihedral torsion parameters to planarize certain types of delocalized trigonal N atoms, such as aromatic aniline. This provides a better match to the time-average molecular geometry in solution or crystal structures. If you are comparing force-field optimized molecules to crystal structure geometries, we recommend using the MMFF94s variant for this reason. All other parameters are identical. However, if you are perfoming “docking” simulations, consideration of active solution conformations, or other types of computational studies, we recommend using the MMFF94 variant, since one form or another of the N geometry will predominate. Finally, the newer "auto" option will cycle through various force-field options starting with MMFF94 until a method succeeds.

Ready to submit your job?

Once you're done just hit the submit button below and let us do the rest.

To submit a job please login or register an account.