Identification of homologous protein models via 3D comparisons using predicted structures

Abstract

Summary: Recent advances in protein structure prediction enable 3D homology alignment and domain annotation using tertiary structures. Here, we present a protocol to identify homologous structures and annotate protein domains through in silico comparisons using the AlphaFold database. We describe steps for downloading and installing PyMOL software, preparing the query structure, and conducting a 3D homology search. The example provided highlights the application of this protocol in reevaluating an mpox viral protein annotation.For complete details on the use and execution of this protocol, please refer to Pan et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Protein Biochemistry
• Structural Biology