Use Foldseek Structural Clustering

Official Neurosnap webserver for accessing Foldseek Structural Clustering online.

Protein Clustering

Overview

The Foldseek easy-cluster algorthim clusters protein structures using a combination of structural and sequence characteristics and allows near full control on search parameters.

Neurosnap Overview

The Foldseek Structural Clustering online webserver allows anybody with a Neurosnap account to run and access Foldseek Structural Clustering, 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.

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Features

  • Structural clustering of PDBs or mmCIFs by creating a structural alignment.
  • Includes advanced filters and thresholds to tailor the clustering to your experimental design.
  • Provides a collection exportable charts of cluster anchors, cluster members, and overall cluster groups.

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 Foldseek Structural Clustering 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 protein structures as PDB or mmCIF files for Foldseek clustering.

The alignment types dictate how the structures are aligned and clustered, 3-Dimensional + Sequence is recommended.

Sensitivity controls the structures reported as matches, the larger the number the more distant structural matches. The sensitivity ranges from 0.00 to 10000 and defaults to 0.001

The minimum sequence identity to be clustered. The sequence identity ranges from 0.00 to 1. The default is zero.

The minimum TMscore of an alignment to be clustered. The TMscore threshold ranges from 0.00 to 1. The default is zero.

The minimum LDDT of an alignment to be clustered. The LDDT threshold ranges from 0.00 to 1. The default is zero.

Ready to submit your job?

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

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