The following API services are provided by Cyrus:
AI Foldingperforms protein structure prediction using the Openfold or Alphafold2 models. 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.
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 database
Clean PDB is a tool made available to all customers free of charge for preparing PDB files for use by the other Cyrus API tools
Designruns 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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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 preparatory to further modeling, or for generating a backbone ensemble for a further modeling experiment.
RosettaHolesruns the RosettaHoles application which produces statistics and visualization of voids in proteins. This is a useful tool for evaluating protein designs.
Single Chain HM is a homology modeling tool for generating a structure prediction for your sequence optimizing structures. This tool adds an additional feature to tell Rosetta where extra disulfides are wanted by the researcher, to cover cases where the templates were not clear. This is appropriate for:
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