Need some help regarding 3d Model predicted by i-tasser?

09 July 2023 1 9K Report

I made a 3d model for IRS2 protein using i tasser software and then refined the predicted model on mod refiner server , But the ramachandran plot score on SAVES serves is not coming in acceptable range (below 85%) of both refined and predicted models. Is there anything I can do next to make 3d Structure more refined and accurate.

NOTE - There are no 3D model available for this protein on PDB server

Mostak Ahamed

If the Ramachandran plot scores for your refined and predicted models are not within the acceptable range (below 85%), there are several steps you can take to further refine and improve the accuracy of your 3D structure:

Molecular Dynamics Simulation: You can consider performing molecular dynamics (MD) simulations on your protein model. MD simulations simulate the physical movements of atoms over time, allowing the structure to relax and reach a more stable conformation. This can help improve the overall quality of your model. There are various MD software packages available, such as GROMACS and AMBER, that you can use for this purpose.

Energy Minimization: Use energy minimization techniques to optimize your protein structure. Energy minimization algorithms aim to find the lowest energy conformation for a given protein structure, which can help improve its stability. Tools like CHARMM, NAMD, or GROMACS can be used for energy minimization.

Model Refinement Tools: Apart from i-TASSER and ModRefiner, there are other tools available for model refinement, such as Rosetta, SwissModel, and Modeller. You can try using these tools to refine your protein model further and generate alternative conformations that may have better Ramachandran plot scores.

Homology Modeling: If you have identified homologous proteins with experimentally determined structures, you can try using their structures as templates for homology modeling. Homology modeling can be performed using software like SWISS-MODEL or MODELLER, which utilize the known structure of a related protein to predict the structure of your target protein.

Expert Review: Consult with experts in the field of protein structure prediction and modeling. They may be able to provide valuable insights and suggest specific methods or tools that can help refine your protein model.

Remember that protein structure prediction and refinement can be a complex process, and it is not uncommon to encounter challenges along the way. It is important to carefully evaluate and validate the refined models using experimental data or additional computational methods.

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