Question: 3D Protein Modelling
gravatar for User 0063
9.8 years ago by
User 0063220
User 0063220 wrote:

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

modeling protein • 2.8k views
ADD COMMENTlink modified 9.8 years ago by Dataminer2.7k • written 9.8 years ago by User 0063220

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

ADD REPLYlink written 9.8 years ago by Pals1.3k
gravatar for Pals
9.8 years ago by
Pals1.3k wrote:

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

ADD COMMENTlink modified 9.8 years ago • written 9.8 years ago by Pals1.3k
gravatar for Dataminer
9.8 years ago by
Dataminer2.7k wrote:

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. ;)

ADD COMMENTlink written 9.8 years ago by Dataminer2.7k
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