Close-up of Puzzle 1076: Vancomycin Binder Design. The vancomycin target is the molecule shown in magenta. The designable unlocked segments of the protein are shown in light green. The locked sections of the protein are shown in dark green. (EnzDes coloring.)
A Binder puzzle is a type of design puzzle in which players design a small protein unit (or a small part of a larger protein) which binds to a protein or other target.
In many binder puzzles, the binder portion is mostly available for design. Some parts of the binder may be locked or held in place by constraints. Most of the segments in the binder are normally mutable. In some puzzles, the binding area is part of a larger protein, in which case much of the protein may be locked, with only certain segments mutable.
The target in a binder puzzle is generally more or less fixed. Much of the target may be locked. It may be possible to wiggle the sidechains of part of the target, but generally the target's backbone has a fixed shape.
The targets of binder puzzle designs have included the antibiotic vancomycin, the Ebola and Marburg viruses, and the Abeta (Aβ) polypeptide associated with the "plaques" found in Alzheimer's disease.
A successful binder design could lead to new drug therapies. In the case of viruses, simply binding to the surface of the virus could prevent the virus from infecting healthy cells. For Alzheimer's disease, binding to the plaques would be a first step toward therapies to either eliminate the plaques or render them harmless.
Here are some examples of binder puzzles with links to the puzzle page in Foldit and the uploaded images here on the wiki.
| puzzle title | Foldit page | results page |
|---|---|---|
| Marburg | ||
| 1144: How low can you go? 10-residue Marburg binder design | 1144 | 1144 |
| 1108: Compact 37-Residue Marburg Virus Inhibitor Design | 1108 | 1108 |
| 1073: Marburg Binder Design with Disulfides | 1073 | 1073 |
| Vancomycin | ||
| 1100: Vancomycin Binder Design: Hydrogen Bond Network | 1100 | 1100 |
| 1076: Vancomycin Binder Design | 1076 | 1076 |
| 1054: Vancomycin Binder: Shape Complementarity | 1054 | 1054 |
| Ebola | ||
| 884b: 74 Residue Ebola Binder Design | 884b | 884b |
| 879: Ebola Binder Design with Disulfides | 879 | 879 |
| Abeta | ||
| 1137: Two-component Abeta binder design | 1137 | 1137 |
| 1010: Abeta Binder Redesign | 1010 | 1010 |
| 976: Abeta binder full-length design | 976 | 976 |
| 811: Abeta Binder Redesign: Round 2 | 811 | 811 |
| 808: Abeta Binder Piecewise Design | 808 | 808 |
| 801b: Abeta Binder Redesign | 801b | |