Analysis of Ab Initio Protein Structure Prediction Methods

Presenter and Co-Authors

Maytha Alshammari, Old Dominion UniversityFollow
Jing He, Old Dominion UniversityFollow

ORCID

0000-0002-1386-5447 (Alshammari)

College

College of Sciences

Department

Computer Science

Graduate Level

Doctoral

Graduate Program/Concentration

Computer Science - Bioinformatics

Publication Date

2023

DOI

10.25883/m5px-tx49

Abstract

Protein structure prediction produces atomic models of three-dimensional structure of a protein from its amino acid sequence. Understanding the function mechanism of proteins requires knowledge of three-dimensional structures. When developing new enzymes and drugs, it's essential to understand the structure of the target protein. In this study, we analyze models predicted using two ab initio protein structure prediction methods, trRosetta and Quark. A set of thirty protein chains was used to evaluate the effectiveness of the methods. The thirty chains were collected from Protein Data Bank (June – November, 2020). The length and the relative position of the predicted secondary structures were examined. We found that the accuracy of models obtained from trRosetta and Quark is good (TM score 0.358 - 0.969). However, in some cases, the methods were not able to accurately predict the relative location of the secondary structures which might affect the overall folding relationship among secondary structures.

Keywords

Ab initio protein structure predictions, trRosetta, Quark

Disciplines

Bioinformatics | Computer Sciences

Files

Recommended Citation

Alshammari, Maytha and He, Jing, "Analysis of Ab Initio Protein Structure Prediction Methods" (2023). College of Sciences Posters. 21.
https://digitalcommons.odu.edu/gradposters2023_sciences/21