A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

Abstract

Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.

Identification of a Novel Dual Inhibitor of Acetylcholinesterase and Butyrylcholinesterase: In Vitro and In Silico Studies

“…To ensure reliable data acquisition, one needs to ensure that the system is stable, and one of the main ways to assess structural stability is by using RMSD graphs. This metric is used to analyze the equilibrium and stabilization of the protein structure and its system during the trajectory of MD simulations [ 31 , 32 , 33 ]. The complexes (ZINC90718 bound to AChE and BuChE) and the APO forms of the proteins were obtained from the RMSD for the main chain (backbone), along with the trajectory (see Figure 5 ).…”