Question: Ab Initio Modelling Of Small Protein
3
gravatar for Priya
8.2 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 • 3.1k views
ADD COMMENTlink modified 8.2 years ago by Flow1.5k • written 8.2 years ago by Priya30
3
gravatar for Kraut
8.2 years ago by
Kraut220
Pittsburgh, PA
Kraut220 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 8.2 years ago by Kraut220
1
gravatar for Khader Shameer
8.2 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 abinitio 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 8.2 years ago • written 8.2 years ago by Khader Shameer18k
1
gravatar for Giovanni M Dall'Olio
8.2 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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

ADD COMMENTlink written 8.2 years ago by Giovanni M Dall'Olio26k
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