Recent Advances in Solving the Protein Threading Problem

TL;DR

This paper discusses recent improvements in protein fold recognition using the FROST tool, highlighting advances in algorithms and computational strategies to efficiently solve large-scale protein threading problems.

Contribution

It introduces new algorithmic approaches and computational methods that enable large-scale protein threading problem solving with improved efficiency.

Findings

Implementation of the most efficient algorithm in FROST

Successful solving of a million instances within reasonable time

Enhanced formulation of the Protein Threading Problem

Abstract

The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms as well. In the recent version of FROST (Fold Recognition Oriented Search Tool) package the most efficient algorithm for solving the Protein Threading Problem (PTP) is implemented due to the strong collaboration between the SYMBIOSE group in IRISA and MIG in Jouy-en-Josas. In this paper, we present the diverse components of FROST, emphasizing on the recent advances in formulating and solving new versions of the PTP and on the way of solving on a computer cluster a million of instances in a easonable time.