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Updated: Jul 6, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Identification of homologous protein models via 3D comparisons using predicted structures
Anyu Pan1, Jieyi Shentu1, Yangfan Zeng1
1State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
Abstract:
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.
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