Template selection

Definition

Template selection is the process of choosing a suitable template structure from a database to model a target protein whose structure is unknown. This choice is crucial because the accuracy of the homology model greatly depends on how closely related the template is to the target in terms of sequence and structural similarity. A good template can lead to a more reliable and functional model, making this step fundamental in homology modeling.

5 Must Know Facts For Your Next Test

1. The quality of the selected template directly influences the accuracy and reliability of the resulting homology model.
2. Template selection often involves searching structural databases like Protein Data Bank (PDB) to find suitable candidates based on sequence similarity thresholds.
3. It's important to consider not only sequence identity but also the overall fold and functional relevance of the template when making selections.
4. Multiple templates can sometimes be used to create more accurate models, particularly when dealing with large proteins or complex domains.
5. The process may also involve assessing the resolution and completeness of the available templates to ensure that they provide a solid foundation for modeling.

Review Questions

• How does the process of template selection impact the overall accuracy of homology modeling?
  • Template selection significantly affects the accuracy of homology modeling because it determines which known structures will be used as references for building the model. If a highly homologous template is selected, the model is likely to be more accurate. Conversely, selecting a less appropriate template can lead to errors in predicting the protein's structure, ultimately impacting its predicted function and biological relevance.
• What factors should be considered when evaluating potential templates for homology modeling?
  • When evaluating potential templates, factors such as sequence identity, structural similarity, functional relevance, and the resolution of available data should be considered. A high percentage of sequence identity suggests greater reliability, while structural alignment reveals how well the template's architecture matches the target. Additionally, ensuring that templates are functionally similar can help create biologically relevant models.
• Evaluate the implications of using multiple templates in homology modeling and how it can improve model quality.
  • Using multiple templates in homology modeling allows researchers to capture diverse structural information that can enhance model quality. This approach can mitigate the risks associated with relying on a single template, particularly when dealing with large proteins or regions with low sequence similarity. By integrating data from various templates, it’s possible to create a more robust and accurate model that better reflects the true conformation of the target protein, leading to improved predictions about its function and interactions.

Related terms

Homology Modeling:

A computational technique used to predict the three-dimensional structure of a protein based on its sequence similarity to one or more known structures.

Alignment: The arrangement of sequences (amino acids or nucleotides) from different proteins to identify regions of similarity that may indicate functional, structural, or evolutionary relationships.

Structural Database: A collection of known protein structures, often used as a reference for template selection in homology modeling.