Knowledge Base

I have a crystal structure with missing loops. I would like to build the loops from a known sequence of residues. What are my options?

If the missing residues are included in the sequence when you import the structure, you can use the Protein Preparation Wizard to fill in the missing loop. Select "Fill in missing loops with Prime" before you click Preprocess. To check whether the missing residues are in the sequence, display the sequence viewer in the Workspace and compare the sequence with the known sequence of your structure.

If the missing residues are not included in the sequence, you should run the protein preparation anyway, as you will have to prepare the structure before you can fill in the loop using other tools.

The easiest option is probably to use the Crosslink Proteins panel, which you can open from the Task Tool (or for 2016-3 and earlier releases, the Tasks menu in BioLuminate or Tasks → Biologics in Maestro). This panel treats the process as cross-linking two protein chains with a linker. The linker in this case is the sequence of missing residues.

  1. In the "Define linker attachment points" section, select each of the "Pick residue in Workspace" options in turn, and pick the residues on either side of the gap. You should pick them in the order in which the missing sequence will be specified (N→C or C→N).
  2. In the "Define monomer set for linker" section, enter the sequence of missing residues in the "Define multi-residue monomer" text box, and click Add to List.
  3. Leave the length of the linker unchanged at the default of one monomer.
  4. Choose a method from the "Linker conformation prediction" option menu, from "Loop lookup" or "Simple de novo loop creation".
  5. Enter a job name and run the job. (A BioLuminate license is required.)

You should refine the resiudes after building them, either with the Protein Refinement tools, or with an MD simulation.

To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.

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