Question: Ab Initio Modelling Of Small Protein
3
gravatar for Priya
9.2 years ago by
Priya30
Priya30 wrote:

Hi,

how do I perform ab initio modelling of a protein with less than 100 amino acids?

modeling protein structural • 3.4k views
ADD COMMENTlink modified 12 months ago by manishagurnani100 • written 9.2 years ago by Priya30

I want to use Swiss Model web tool for modelling a protein of interest. What are the steps and precautions?

ADD REPLYlink written 12 months ago by manishagurnani100

Please open a new question after reading the available on materials towards this tool and using the search function to find previous threads. Brief Reminder On How To Ask A Good Question

ADD REPLYlink written 12 months ago by ATpoint34k
4
gravatar for Kraut
9.2 years ago by
Kraut230
Pittsburgh, PA
Kraut230 wrote:

Rosetta is probably the most widely used program for this problem. It performs very well in many macromolecular modeling problems including Ab initio. You get the software from http://www.rosettacommons.org/. RosettaCommons also has tutorials, examples, and a user forum. The methods have been described in dozens of journal articles.

ADD COMMENTlink written 9.2 years ago by Kraut230
2
gravatar for Khader Shameer
9.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Not sure if the currently available abinitio methods are mature enough to model a full-length protein of 100 residues. I would suggest you to decompose your sequence into secondary structure elements using tools like PSIPRED. Then identify all loop residues and model loops separately using loop modelling approaches and model the remaining residues using ab initio approach.

You may also interested in a web server based on the Rosetta method. Robetta: Full-chain protein structure prediction server. It uses a hybrid approach to model query sequence. Detailed help page is available here.

ADD COMMENTlink modified 6 months ago by RamRS27k • written 9.2 years ago by Khader Shameer18k
1
gravatar for Giovanni M Dall'Olio
9.2 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

You can try the Swiss-Model web tool, try with the 'Automated mode' to be started.

ADD COMMENTlink written 9.2 years ago by Giovanni M Dall'Olio27k
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