ClusCo: clustering and comparison of protein models

TL;DR

ClusCo is a fast, high-throughput software tool designed for efficient comparison and clustering of protein models, significantly accelerating the protein structure validation process using optimized C/C++ code and parallel computing.

Contribution

The paper introduces ClusCo, a novel software that enables rapid all-versus-all protein model comparison and clustering, optimized for high-throughput processing with CPU and GPU acceleration.

Findings

ClusCo achieves significant speedup over existing tools.

Supports multiple similarity measures including cRMSD, GDT_TS, TM-Score.

Effective for large-scale protein model validation and analysis.

Abstract

Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline. Results: Clusco is fast and easy-to-use software for high-throughput comparison of protein models with different similarity measures (cRMSD, dRMSD, GDT_TS, TM-Score, MaxSub, Contact Map Overlap) and clustering of the comparison results with standard methods: K-means Clustering or Hierarchical Agglomerative Clustering. Conclusions: The application was highly optimized and written in C/C++, including the code for parallel execution on CPU and GPU version of cRMSD, which resulted in a significant speedup over similar clustering and scoring computation programs.