Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors

Neural network (NN)-based protein modeling methods have improved significantly in recent years. Although the overall accuracy of the two non-homology-based modeling methods, AlphaFold and RoseTTAFold, is outstanding, their performance for specific protein families has remained unexamined. G-protein-coupled receptor (GPCR) proteins are particularly interesting since they are involved in numerous pathways. This work directly compares the performance of these novel deep learning-based protein modeling methods for GPCRs with the most widely used template-based software—Modeller. We collected the experimentally determined structures of 73 GPCRs from the Protein Data Bank. The official AlphaFold repository and RoseTTAFold web service were used with default settings to predict five structures of each protein sequence. The predicted models were then aligned with the experimentally solved structures and evaluated by the root-mean-square deviation (RMSD) metric. If only looking at each program’s top-scored structure, Modeller had the smallest average modeling RMSD of 2.17 Å, which is better than AlphaFold’s 5.53 Å and RoseTTAFold’s 6.28 Å, probably since Modeller already included many known structures as templates. However, the NN-based methods (AlphaFold and RoseTTAFold) outperformed Modeller in 21 and 15 out of the 73 cases with the top-scored model, respectively, where no good templates were available for Modeller. The larger RMSD values generated by the NN-based methods were primarily due to the differences in loop prediction compared to the crystal structures.