I had run homology modelling on unknown protein structure using I-Tasser and Robetta. Both are consensus that the mutation on the protein is at the loop part of the protein. However, the structure of the loop protein and other part of protein is not similar. But both structure is fulfill the criteria of Ramachandran plot. So, this make me difficult to choose which one is the exact structures. Since the protein sequence more than 1500a amino acids, I separate the sequence to two parts for I-Tasser. For Robetta, I predicted the domain first before proceeded with homology modelling for each domain. Only the first 5++ amino acids had crystallized structure but the mutation is at 7++ and no available structure is suitable as template. Thank you for your time.
In your case, since both I-Tasser and Robetta predict that the mutation is located in a loop region of the protein, it's possible that the loop region is structurally flexible and can adopt different conformations. Additionally, it's possible that the loop region is not well conserved among homologous proteins, which can make it difficult to identify suitable templates for homology modeling. To choose the most reliable model, you can consider several factors, such as the quality of the model as assessed by various metrics (e.g., MolProbity, QMEAN), the completeness of the model (e.g., missing residues or side chains), the accuracy of the active site and other important regions, and the degree of similarity to available experimental structures (if any). It may also be helpful to perform molecular dynamics simulations or other validation methods to assess the stability and flexibility of the models and to further refine the models if necessary. Finally, it's important to keep in mind that homology modeling is a computational prediction method and the resulting models should be considered as hypotheses that require experimental validation.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Proteins