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AI Foldingperforms protein structure prediction using the Openfold or Alphafold2 models Openfold, AlphaFold, and ESMFold. Protein structures are optionally relaxed using Rosetta, and a molprobity report is produced for each model.
Antibody HM creates homology models of antibodies using the Cyrus NextGen Antibody structure prediction method.
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This method takes as input an antibody heavy and light chain and returns models of the antibody fV fragment. The Single Chain HM API is a more suitable approach for modeling nanobodies and non-antibody proteins.
BLAST runs the BLAST+ executable with the v5 NCBI databasedatabases.
Clean PDB is a tool made available to all customers free of charge for preparing PDB files for use by the other Cyrus API toolsDesignruns the Rosetta FastDesign protocol with a PDB file and a resfile as input.
DDG is a tool for predicting the energetic consequences of single mutations. It approximates the Gibbs free energy change of folding of the native vs. point mutant.
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Design is a tool for performing Rosetta based protein design using the FastDesign protocol.
Disulfidizer is a tool for searching for disulfides. Given an input structure it will attempt to sample disulfides that might exist. This is appropriate for:
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Disulfidizer results are reasonably polished (if the –permissive flag is not used), but you may wish to further evaluate disulfides with other computational tools before proceeding to a wet experiment.
Epitope Scan runs an rosetta the Rosetta MHC II epitope prediction algorithm, as well as the NetMHCPan and NetMHCIIPan prediction algorithms on an input protein structure or sequence. This This API uses a machine learning model to predict epitopes based entirely on the sequence of the protein. Structure input is provided as a convenience but the API will produce identical results regardless of whether a sequence or structure is used as input.
Force Disulfide forces the input disulfide to exist and attempts to relax the protein structure in the presence of that chemical bond (simulated as bond-like restraint, not a kinematic imperative). It requires the user to state which disulfides are desired. This tool is appropriate in three cases:
You know this bond forms in nature for this sequence (perhaps from mutational data), have a structure of the sequence without cysteines or disulfides, and want a quick peek at what it might look like
You are doing blue-sky thinking or hypothesis generation about places disulfides could go and want to absolutely force models to have a given disulfide (our other tools will not enforce it so strongly if the energetics dislike it)
You are creating input models for other tools like HM.
Force disulfide results should always be considered preliminary and evaluated with/after other modeling tools.
Glyocosylation prediction Is a tool for predicting predicts glycosylation sites using a Cyrus-developed version of DeepNGlyPred (DNGP)-- a deep neural-network (DNN) learning tool for sequence-based human N-linked glycosylation prediction.
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Make Fragments creates Rosetta Fragments files fragment libraries for use in Rosetta structure prediction and modeling protocols.
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Relax runs the Rosetta FastRelax protocol. Quoting from the RosettaCommons documentation: “This finds low-energy backbone and side-chain conformations near a starting conformations by performing many rounds of packing and minimizing, with the repulsive weight in the scoring function gradually increased from a very low value to the normal value from one round to the next.” This is useful for taking a structure not generated by Rosetta and “relaxing” it into the Rosetta scorefunction score function preparatory to further modeling, or for generating a backbone ensemble for a further modeling experiment.
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Tolerance Identificationfinds the closest sequence fragments in the human genome which are present in . your protein of interest, this tool is used to screen protein designs for immune tolerance.
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