See here on the blog a description
How to fold a protein in a puzzle with predicted contacts.Edit
On this kind of puzzle, the way to get a high score is to try to match the structure with the contact map. A contact map is an n x n graph with segments 1 to n and black dots showing which segments of your puzzle are close to each other. Colored squares indicate which segments should be close together. A dark color indicates great probability or proximity. A light color indicates weak probability or "heat". Many examples of contact maps and related 3D structures for known proteins are shown here.
Puzzles with predicted contacts and an exploration multiplier
by Timo van der Laan
On this kind of puzzle, the way to get a high score is to have a big multiplier.So I started by placing sheets together that according to the map should be together.Look in the pictures below to see how the multiplier changes and what parts of the map are getting filled.
See this article with some pictures: Protein contact map prediction using multi-stage hybrid intelligence inference systems - Anas A. Abu-Doleha, Omar M. Al-Jarraha, Asem Alkhateebb