3D Protein Modelling

Question

[User 0063]

Dear all,

I'm looking for a tutorial/book/document for learning intermediate and advanced tips in manual 3d protein modelling with Deep Viewer or Swiss Pdb viewer.

For instance, how can i solve in case of gaps, Nonplanar Peptide Bond, Missing Main-Chain Atoms, Missing Side-Chain ?

How can I use disorder prediction, secondary structure prediction, solvent accessibility prediction, kinke proline prediction, topology prediction during 3d modellation

I hope you can help me anyway.

Thank you

[Pals]

Have you found the template for your sequence? What is the sequence identity?

Answer 1

[Pals]

I would have some recommendations based on what I basically use.

For general overview on homology modeling this Biobook might be helpful.

For tutorials on Deep-View Swiss-PDB Viewer you can access tutorials from Tutorial on Deep-View Swiss-PDB viewer.

For editing gaps, you might need to make multiple sequence alignment and look at the sequence conservation. Some information can be found here. For Secondary structure prediction Psipred and Jpred are highly recommended. In addition, you can look into Expasy repository for a number of prediction tools Expasy tools

Answer 2

[Dataminer]

Have a look at this nature article. By the way, may I ask why you only want to learn through Swiss PDB or Deep View and why not modeller or I-Tasser. Although I-Tasser is an automated server but you can still provide your own alignment of target and template. You must be knowing, quality of alignment is crucial for good modelling, which indeed means selection of good templates. It is worth trying different softwares for modelling and then compare it by evaluating on servers like SAVS or others.

Let me know if you have more questions.

Happy modelling. ;)