Use LigandMPNN

Official Neurosnap webserver for accessing LigandMPNN online.

Inverse Folding Protein Design

Overview

LigandMPNN is an inverse folding model that is capable of not only predicting the amino acids of a protein structure, but also certain chains, and complexes. Additionally, LigandMPNN can be used as a way to create functional homologs / mutants of existing proteins by inverse folding their structures and sampling the sequence space.

Neurosnap Overview

The LigandMPNN online webserver allows anybody with a Neurosnap account to run and access LigandMPNN, 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

  • Sucessor of ProteinMPNN service.
  • Supports LigandMPNN, ProteinMPNN and SolubleMPNN.
  • Allows you to specify fixed chains and positions.
  • Allows you to inverse fold any protein or complex of proteins.
  • Supports different sampling techniques to better explore the protein landscape.
  • Includes per sequence metrics like overall confidence and sequence recovery.
  • Includes amino acid probabilities by position.

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 LigandMPNN 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 protein structure to predict the amino acid sequence of.

Design Options

Fixed positions are positions that will not be inverse folded or affected in anyway by ProteinMPNN. This option allows you to specify which chains, residues, and residue ranges should be fixed. To fix an entire chain simply enter the chain's ID (e.g., "C" to fix all residues of chain C). To fix specific positions use <chain ID><residue ID> (e.g., A10 to fix residue 10 on chain A). To fix a range of residues use <chain ID><start residue ID>-<end residue ID> (e.g., A10-20 will fix all residues between 10 and 20 on chain A). Multiple positions, chains, and ranges can be fixed all at once by comma delimiting your options (e.g., A15,A20-23,B will fix residues 15, 20, 21, 22, 23, and all residues on chain B).

Invert the selected fixed positions above. If you decide to fix a position like A1-10 above and enable this mode then instead of fixing A1-10, everything will be fixed except for A1-10.

The number of output sequences to generate.

Specify sampling temperature lower numbers produce higher probability sequences, higher numbers produce more diverse sequences. A sampling temperature greater than 1.0 means random sampling.

Advanced Settings

Select the model you want to use to predict sequences with. The best performing is typically either 0.3Ã… or 0.2Ã… (according to the ProteinMPNN paper).

Specify amino acid(s) to exclude (example: "C,A,T").

The default value, 0, will use a random seed. A random seed will generate different results on the same instructions. Setting the seed allows for experiment design changes.

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