Aflatoxin B1 JMol

Aflatoxin, a small molecule ligand seen in the Aflatoxin Challenge puzzles.

This page offers a slightly wonky definition of a ligand and offers some strategies. See ligand for a concise definition.

What is a Ligand?Edit

A ligand is the coordinational bond between an ion or a smaller molecule containing a metal ion which offers electron pairs and creates a spacial coordination with surrounding atoms. Foldit, however, doesn't have metallic atoms, so ligands aren't registered the same way. Steric comformity and polar interaction is usually of most importance for foldit's ligand puzzles.

How to band downEdit

Bands can help you move around and position the ligand in respect to its environment. For the best result, you should use at least 2 bands. You can either let the band move the ligand around by doing wiggle backbone/all, or you can pull the ligand around closer to the target. After getting your ligand to the position desired, you can click D (disable/enable band) every 2 seconds while wiggle all is on.

How to move and whyEdit

You can use bands

Tweeking the sidechains to move ligand gently. By pulling on the sidechains of the ligand you can more gently rock or pull and then let the ligan resettle into a new position. This may help gain points.

Also by tweaking the surrounding sidechains help to reduce the overall voids.

Mutating the surrounding sidechains.Edit

Some ligand puzzles allow you to mutate the surrounding residues around the ligand. In such puzzles, you may want to try and manually mutate these segments or allow for a script to find the best stericity, aromatic and polar interaction.

Why all those red constraint lines and what to do about itEdit

When the Ligand is moved to far away often red constraint lines apear. These mean that some needed bands are broken. By placing bands along the red lines and wiggleing the backbone the bonds can be brought together once again.

Twisting and turning the ligandEdit

Certain ligand are big enough to be flexible, so you can try to twist them around to get a better stericity=less clashes.

Ligand movementEdit

Moving the ligand get you extra points. It may have to apply brute force. Pull and tug on it, or twist it around and let it settle back. Pulling gently on a sidechain can shake the ligand and let it find a new energy (and more points).

A method used on some interface puzzles with only the ligands moveable was to band the ligand to the sidechains. The ligand's H-bonding atoms are banded to nearby sidechains that can H-bond with the ligand. This may take several strong bands. Once the ligand is banded in the place you want it to be, enable/disable the bands rapedly, and wiggle, mutate, wiggle out.

More techniques at > The Foldit Labs

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