Additional Workflows

Workflows for rescoring protein-protein complex from other software, and disulfide bond removal with maintained overall stability:

Rescore Protein-Protein Complex from Other Software

  1. Run 3 Repack repetitions on complex and Minimize each. Download lowest Score (AB_Score)
  2. Run same as 1 on individual proteins not in complex and download A_Score and B_Score
  3. Complex_Score = AB_Score – (A_Score + B_Score)

Disulfide Bond Removal with Maintained Overall Stability

  1. Edit PDB file to change the three-letter name at each disulfide from CYS to ALA and note Residue_Positions
  2. Load edited PDB into Bench and run Prepare
  3. Select Residue_Positions and run Design to allow for all residues except CYS
    1. For higher accuracy, also select spatial neighbors and set them to self (no mutation, but Design will repack). This is design with local Repack
  4. For increased diversity, try multiple Prepares, and then Design/Minimize/Design cycles.

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