Recovery of Protein Structure from Contact Maps

TL;DR

This paper introduces an efficient algorithm for reconstructing 3D protein structures from contact maps, demonstrating its effectiveness with both physical and corrupted maps, and analyzing the impact of contact reduction.

Contribution

The paper presents a novel algorithm capable of accurately recovering protein structures from contact maps, including corrupted ones, advancing protein folding prediction methods.

Findings

Reconstructed structures closely match original when using physical contact maps.

The method effectively recovers underlying structures from corrupted contact maps.

Structure quality degrades gracefully with fewer contacts.

Abstract

We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose contact map is essentially similar to the target. Furthermore, the reconstructed and original structures are similar up to the resolution of the contact map representation. Next we use non-physical target maps, obtained by corrupting a physical one; in this case our method essentially recovers the underlying physical map and structure. Hence our algorithm will help to fold proteins, using dynamics in the space of contact maps. Finally we investigate the manner in which the quality of the recovered structure degrades when the number of contacts is reduced.