Dihedral Angle Adherence: Evaluating Protein Structure Predictions in the Absence of Experimental Data

2024/07/09 by Musa Azeem, Azeem, Musa, Homayoun Valafar +1
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Biomolecules (q-bio.BM) #Computational Engineering #FOS: Biological sciences #FOS: Computer and information sciences #Finance #Machine Learning in Bioinformatics #Protein Structure and Dynamics #and Science (cs.CE)

paper · pdf · doi:10.48550/arxiv.2407.18336

openalex publication_date 2024/07/09 · openalex created_date 2024/09/12 · openalex updated_date 2026/07/28

Abstract

Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge. The traditional method, RMSD, relies on experimentally determined structures and lacks insight into improvement areas of predictions. We propose an alternative: analyzing dihedral angles, bypassing the need for the reference structure of an evaluated protein. Our method segments proteins into amino acid subsequences and searches for matches, comparing dihedral angles across numerous proteins to compute a metric using Mahalanobis distance. Evaluated on many predictions, our approach correlates with RMSD and identifies areas for prediction enhancement. This method offers a promising route for accurate protein structure prediction assessment and improvement.

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