CLP-based protein fragment assembly

TL;DR

This paper presents a novel CLP-based method for protein 3D structure prediction using fragment assembly, leveraging a constraint solving approach with a discretized protein model, demonstrating feasibility and efficiency.

Contribution

It introduces a constraint logic programming framework for protein folding that incorporates a new fragment database and a discretized protein model for efficient assembly.

Findings

Method is feasible and efficient for protein structure prediction.

The approach allows easy extensions for improved accuracy.

Constraint solving effectively models the fragment assembly process.

Abstract

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.