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Recipe: Lig Detector 1.1
Created by LociOiling 2 2
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Name: Lig Detector 1.1
ID: 102541
Created on: Sat, 11/11/2017 - 23:56
Updated on: Sat, 11/11/2017 - 23:56
Description:

Detects ligands and flags suspicious ligands. Tries to determine whether a ligand is modifiable. Flags ligands which aren't at the end of the protein or which have a standard amino acid code.



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LociOiling's picture
User offline. Last seen 1 hour 9 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
better detection for current ligand puzzles

Lig Detector was originally created to detect spurious ligands created by a bug in the auto structures tool.

Recent Foldit puzzles have brought back ligands in a big way. The puzzles in the aflatoxin series have a small molecule ligand. Puzzle 1443: Classroom Puzzle: Engineer the Active Site featured a small molecule ligand plus three metal atom ligands.

Puzzle 1446: Y1 Receptor Ligand Docking featured a modifiable ligand that could take different shapes, and even reported multiple rotamers, like an amino acid sidechain. The major goal of the puzzle was finding the best shape and position for the ligand.

In previous puzzles, the ligand had always been locked or otherwise unchangeable.

The new version of Lig Detector hunts for ligands as before, but now looks at things like locked status, atom count, and rotamer count to determine whether a ligand is likely to be modifiable.

As before, Lig Detector flags any ligands which aren't at the end of the protein. (This happened once, on a puzzle from long ago.)

In case the auto structures bug comes back, Lig Detector checks the AA code of each ligand. A ligand with one of the 20 familiar amino acid codes is probably a mistake or the return of a old defect.

There are some quirks.

Some ligands show up in "locked" colors. The function structure.IsLocked tells you these ligands are locked.

Other ligands have normal colors, but you get "sidechain is locked" if you try to drag them. IsLocked thinks they're unlocked.

There's currently no way to detect a locked sidechain in a recipe.

To work around the locked sidechain issue, the recipe looks at the rotamer count in addition to the locked status to determine whether a ligand is modifiable. A rotamer count of one (or less) indicates a non-modifiable ligand.

Another quirk is single-atom ligands. In puzzle 1443, there were three ligands which were supposed to be zinc atoms. But structure.GetAtomCount reported five atoms for each. The extras were "virtual" atoms, which represented how the zinc would be bonded.

To allow for virtual atoms, any ligand with five atoms or less is assumed to be a single-atom metal ligand, non-modifiable.

Regardless of whether a ligand is modifiable, it may affect scoring if it gets close to the protein. Recipes should consider carefully whether to skip ligands.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons