Equipping Decoy Generation Algorithms for Template-free Protein Structure Prediction with Maps of the Protein Conformation Space

9 pages•Published: March 18, 2019

Abstract

A central challenge in template-free protein structure prediction is controlling the quality of computed tertiary structures also known as decoys. Given the size, dimensionality, and inherent characteristics of the protein structure space, this is non-trivial. The current mechanism employed by decoy generation algorithms relies on generating as many decoys as can be afforded. This is impractical and uninformed by any metrics of interest on a decoy dataset. In this paper, we propose to equip a decoy generation algorithm with an evolving map of the protein structure space. The map utilizes low-dimensional representations of protein structure and serves as a memory whose granularity can be controlled. Evaluations on diverse target sequences show that drastic reductions in storage do not sacrifice decoy quality, indicating the promise of the proposed mechanism for decoy generation algorithms in template-free protein structure prediction.

Keyphrases: decoy generation, decoy quality, evolutionary algorithm, template free protein structure prediction

In: Oliver Eulenstein, Hisham Al-Mubaid and Qin Ding (editors). Proceedings of 11th International Conference on Bioinformatics and Computational Biology, vol 60, pages 161-169.

Links:	https://easychair.org/publications/paper/Vcvg
	https://doi.org/10.29007/j5p9