Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.

ABSTRACT:

Motivation

The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2 (AF2). However, for many targets, AF2 models still have room for improvement. In previous CASP experiments, highly computationally intensive MD simulation-based methods have been widely used to improve the accuracy of single 3D models. Here, our ReFOLD pipeline was adapted to refine AF2 predictions while maintaining high model accuracy at a modest computational cost. Furthermore, the AF2 recycling process was utilized to improve 3D models by using them as custom template inputs for tertiary and quaternary structure predictions.

Results

According to the Molprobity score, 94% of the generated 3D models by ReFOLD were improved. AF2 rec

SUBMITTER: Adiyaman R 

PROVIDER: S-EPMC10290552 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature