by Joe Ylagan | Apr 19, 2024 | Structure Prediction
OVERVIEW Full Length Antibody HM is a structure prediction tool that creates homology models of antibodies using the Cyrus NextGen Antibody structure prediction method. RUNNING FULL LENGTH ANTIBODY HM To begin, open an existing project or create one in CAD. Click on...
by Ben Baker | Mar 21, 2024 | Structure Prediction
OVERVIEW AI Folding provides a common interface to AI based protein structure prediction tools. It currently supports OpenFold, AlphaFold, and ESMFold. RUNNING AI FOLDING Begin by opening a project in CAD and select the AI Folding button located to the right under...
by Sam | Oct 23, 2020 | API
This documentation is deprecated, please use the new documentation site instead. The solubility scoring API predicts the solubility of an input protein structure. Inputs Input PDB file — a PDB file with the residues starting at 1 and increasing monotonically...
by Sam | Oct 23, 2020 | API, Uncategorized
This documentation is deprecated, please use the new documentation site instead. The Relax API runs the Rosetta FastRelax protocol. Quoting from the RosettaCommons documentation: “This finds low-energy backbone and side-chain conformations near a starting...
by Sam | Oct 23, 2020 | API
This documentation is deprecated, please use the new documentation site instead. The epitope scan API runs the rosetta MHC II epitope prediction algorithm on an input protein structure or sequence. This API uses a machine learning model to predict epitopes based...
by Sam | Oct 23, 2020 | API
This documentation is deprecated, please use the new documentation site instead. 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 tool is suitable for...
by Sam | Sep 30, 2020 | API
This documentation is deprecated, please use the new documentation site instead. The antibody homology modeling API creates homology models of antibodies using the Cyrus NextGen Antibody structure prediction method. This method takes as input an antibody heavy and...
by Sam | Sep 29, 2020 | API
This documentation is deprecated, please use the new documentation site instead. The force disulfide protocol mutates a specified set of residue pairs to cysteines, forms disulfide bonds between them, and then performs a constrained Rosetta relaxation of the entire...
by Sam | Sep 29, 2020 | API
The Cyrus API The Cyrus API is a cloud based system that runs molecular modeling protocols developed by Cyrus Biotechnology. Each service in the API shares a common interface for submitting and managing jobs as well as retrieving results. A Command Line Application...
by Sam | Sep 29, 2020 | API
This documentation is deprecated, please use the new documentation site instead. The disulfide single chain homology modeling API creates homology models of single chain proteins using the Rosetta hybridize homology modeling method. By default, the hybridize method...
