API Documentation

AI Folding API

The AI Folding API provides a common interface to AI based protein structure prediction tools. The API currently supports OpenFold, AlphaFold2, and ESMFold. ...

Anarci API

The Anarci API runs the Antigen receptor Numbering And Receptor ClassificatIon tool for numbering amino-acid sequences of antibody and T-cell receptor variab...

Antibody HM API

The Antibody HM API is our most high resolution structure prediction tool for an antibody variable region. The “NextGen” antibody software developed by Levit...

API Services

The following API services are provided by Levitate:

BindCraft API

The BindCraft API provides an interface to the BindCraft protein binder design tool. This tool takes as input a target PDB file and generates new novel prote...

BLAST API

The BLAST tools API runs standalone BLAST+ executables with v5 NCBI databases for design related queries. Three modes are available: nopssm, pssm, and patent...

Boltz1 API

The Boltz1 API provides an interface to access the Boltz1 structure prediction tool. Boltz1 is the first open source, commercially available, replication of ...

Clean PDB API

The Clean PDB API is made available to all Levitate Engine API customers free of charge. Use of Clean PDB does not count towards yearly request quotas.

Colab Search API

The Colab Search api runs the MSA generation tool developed by the team at ColabFold on a private server. MSA generation is required step for many ai protein...

Command Line

The lev command line application that is used to submit API commands, retrieve the results, and check the status of running jobs.

DDG API

The DDG API runs the Rosetta Cartesian DDG protocol. The cartesian DDG protocol is described in Prediction of Protein Mutational Free Energy: Benchmark and ...

Deimmunizer API

The Deimmunizer API runs the Cyrus MHC Class II deimmunization protocol on a given protein. Designable residues are defined with a residue file (resfile). Mu...

Design API

The Design API runs the Rosetta FastDesign protocol given an input PDB file and a residue file (resfile). FastDesign performs FastRelax with design enabled t...

Disulfidizer API

The Disulfidizer API runs the Rosetta “Disulfidizer” protocol. The disfulfidizer protocol attempts to stabilize a protein by making disulfide bonds. This met...

Epitope Scan API

Please note that NetMHCPan and NetMHCIIPan modes are only available for users with a valid DTU Health Tech license agreement.

Force Disulfide API

The force disulfide protocol mutates a specified set of residue pairs to cysteines, forms disulfide bonds between them, and then performs a constrained Roset...

Glycosylation Prediction API

In order to improve the success of and confidence in designed glycosylation sites, Cyrus has implemented glyco-predictor, an in-house version of DeepNGlyPred...

Installation

Below are specific instructions for installing the application in Windows, MacOS, and Linux

Interface Analyzer API

The Interface Analyzer API runs either Rosetta InterfaceAnalyzer or the Rosetta semi-explicit water protocol on a given structure for a defined protein-prote...

LigandMPNN API

The LigandMPNN API provides an interface to the LigandMPNN protein design tool. This tool is the latest version of the MPNN based design tools and is capable...

Loop Modeling API

The Loop Modeling API runs the Rosetta Next Generation KIC loop modeling protocol. This API is useful for modeling loops of between 5 and 17 residues. This...

Make Fragments API

The make fragments API generates Rosetta fragment libraries based on an input sequence.

Molprobity API

The Molprobity API takes as input a PDB file and runs MolProbity with the default settings, returning an HTML report. This tool is useful for identifying iss...

ProteinMPNN API

The ProteinMPNN API provides an interface to the ProteinMPNN protein design tool. This tool takes as input a PDB file and rapidly generates new sequences pre...

Radius Of Gyration API

The Radius Of Gyration API provides an interface to score a protein structure in Rosetta using the Radius of Gyration score term. This is frequently used to ...

Relax API

The Relax API runs the Rosetta FastRelax protocol. This is useful for taking a structure not generated by Rosetta and “relaxing” it into the Rosetta scorefun...

How to Create a Resfile

Design and Deimmunizer will sample mutations in a protein based on the instructions defined in a resfile. The file will be included when the design job is su...

RF2NucleicAcid API

The rf2-nucleic-acid API provides an interface to access the RoseTTAFold2 Nucleic Acid tool. The source code and additional documentation can be found on the...

RFAllAtom API

The RFAllAtom API provides an interface to access the RoseTTAFoldAllAtom folding tool. This tool is used for structure prediction of complexes involving both...

RFAntibody API

RFAntibody is a set of tools for the de novo design of antibodies. The system consists of specially tuned versions of RFDiffusion, ProteinMPNN, and AlphaFol...

RFDiffusion All Atom API

The RFDiffusionAllAtom API runs RFDiffusionAllAtom on an input template PDB file. Like RFDiffusion RFDiffusionAllAtom is a method for structure generation (w...

RFDiffusion API

The RFDiffusion API runs RFDiffusion on an input template PDB file. RFDiffusion is a method for structure generation (with or without conditional information...

Rosetta Holes API

The RosettaHoles API runs the RosettaHoles application (See RosettaHoles for details) on an input PDB file. RosettaHoles is an application which identifies v...

RosettaScripts API

The RosettaScripts API runs RosettaScripts XML scripts. This API allows you to run almost any Rosetta protocol through the Engine API framework.

Single Chain HM API

The Single Chain HM API creates homology models of single chain proteins using the Rosetta hybridize method. By default, Rosetta hybridize will automatically...

Template Predictor API

The Template Predictor API runs BLAST, SparksX, and HHsearch. It will output a HHR sequence alignment file, one alignment file from hhsearch and one from spa...

ThermoMPNN API

The ThermoMPNN API provides an interface to the AI based ThermoMPNN protocol for performing a full site saturation mutagenesis (SSM) DDG analysis of a protei...

Tolerance Identification API

The Tolerance Identification API finds the top N closest (by Blosum62) N-mers in the human genome against a given protein of sequence.