Table 1.

Summary of established protein modeling.

Method	Advantages	Disadvantages	Examples
Homology Modeling	1. Utilizes experimentally determined structures of homologous proteins. 2. Highly accurate when suitable templates are available. 3. Widely used and accessible.	1. Relies on the availability of suitable templates. 2. Less reliable for unique proteins lacking close relatives in the database. 3. Less effective for exceptionally large or structurally complicated proteins.	Swiss-Model [32], Modeller [33], Phyre2 [34]
Ab Initio Modeling	1. Predicts structure solely from amino acid sequence, no need for existing templates. 2. Effective in producing models for proteins with limited sequence identity to known structures. 3. Can explore vast conformational spaces to identify low-energy protein structures.	1. Computationally intensive. 2. Success depends on the accuracy of energy functions and sampling algorithms. 3. May struggle with proteins with novel folds or significant structural rearrangements.	Rosetta [35], QUARK [36], I-TASSER [37,38,39,40]
Threading	1. Considers both sequence and structural information for template selection. 2. Predicts structures for proteins with limited sequence similarity to known structures. 3. Increases the scope of prediction to include proteins with diverse sequences and folds.	1. Requires significant computational resources for template search and alignment. 2. Relies on the accuracy of threading algorithms and the structural compatibility of templates. 3. May produce inaccurate models if no suitable templates are found.	I-TASSER [37,38,39,40], HHpred [41], Phyre2 [34]