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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.
Deimmunizer is a Rosetta based tool for reducing immunogenicity of proteins by reducing predicted MHC Class II epitopes.
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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Force disulfide results should always be considered preliminary and evaluated with/after other modeling tools.
Glyocosylation prediction Is a tool for predicting 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.
Loop modeling 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 resampling the conformations of existing loops. It is the same underlying tool as our Loop Rebuild Action in Bench; that tool’s documentation contains more details.
Make Fragments creates Rosetta Fragments files for use in Rosetta structure prediction and modeling protocols.
Molprobity generates HTML reports using the MolProbity software developed at Duke University (http://molprobity.biochem.duke.edu/ )
Post-Translational Modification Prediction quickly predicts glycosylation, isomerization, Asn deamidation, and Met photooxidation sites to identify manufacturing liabilities in proteins.
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.
RfDiffusion Runs the Rosetta RFDiffusion AI protein design protocol.
RosettaHolesruns the RosettaHoles application which produces statistics and visualization of voids in proteins. This is a useful tool for evaluating protein designs.
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Template Predictorruns blast, sparksX, and hhsearch, and returns alignment information which can be useful in determining how well homology modeling will work for the given target.
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.