Protein structure & folding information exploited from remote homologs.

Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway.

This tool is known as PAthreader [1]. It recognizes remote templates and explores their folding pathways. A summary of the PAthreader workflow is explained below.

How PAthreader works?

• PAthreader extracts predicted distance profiles and structure profiles from PDB and AlphaFold DB.
• Creates a three-track alignment between them to improve recognition accuracy.
• Improves AlphaFold2 performance by using the templates identified by PAthreader.
• Later, it explores the protein folding pathways based on the hypothesis that dynamic folding information of protein is implicitly contained in its remote homologs.

The results show higher accuracy than the HHsearch and PAthreader outperforms AlphaFold2 in accuracy [1].

The online server of PAthreader is freely available at http://zhanglab-bioinf.com/PAthreader/. The code is freely available on GitHub.

For further details, read here.

References

1. Zhao, K., Xia, Y., Zhang, F. et al. (2023). Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Commun Biol 6, 243.