Hi Toluwase,

Why not to put in the BLAST search and see what you will get?

If this is a functional structure, most likely the Nature already used similar sequences for this. Your goal would be to find sequence homologs and search functional active proteins among found sequences.

https://www.uniprot.org/blast/

George.

Rosetta Protein Design is your tool of choice for this task: https://www.rosettacommons.org/demos/latest/tutorials/protein_design/protein_design_tutorial

Dear Toluwase,

Please get a professional system. I would recommend Schroedinger LLC Maestro suite and the Proten Wizard prep module. The academic version may correct some common mistakes and give you a good approximation of the problem. The version is free for academia.

The other option is to use a public tool. There are plenty of those but not at the level I would spend my money to synthesize genes for my work. try SwissModel, Chimera and Modeler, and Phyre2 server. The last one does a wonderful job in intensive mode but is still short when it comes to Maestro.

Good luck,

Wes

@Wieslaw Swietnicki, the tools you suggested are OK for homology modeling of

@Wieslaw Swietnicki, @George Minasov: the tools you suggested are OK for assigning a structure to a natural or slightly modifies sequence. However, to assign a sequence to a novel, designed framework you need different tools. These tasks are not well supported by professional systems, as they are not yet routinely used in the pharmaceutical industry. Look at the work of the Baker group on ab-initio design of novel proteins.

Dear Annemarie,

Thanks for the info. I know about Rosetta from other sources. David's approach is more sophisticated and requires a massive computational support. My friend tried it in US and he had an HPC cluster from a secret place for his disposal. Suggesting such a solution to a beginner would not be helpful.

Commmercial tools are OK for slight modifications as you have suggested. I thought it should be a good start for that person instead of a custom made solutions requiring a different set of skills.

Best regards,

Wes

Well, the op clearly stated in his title that he is working on a designed structure. Therefore I based my answer on this information, assuming that he works in an environment familiar with protein design. He stated "I have a sequence already obtained from the designed protein structure but want to explore the sequence space for other possible sequences to work with", which in first approximation would be a task for rosetta fixbb. I choose to point him at the tutorial rather than the directly at the fixbb server (http://rosettadesign.med.unc.edu) since I thought he should first read up on principles used. I frequently run fixbb jobs on the spare cores of my mac - they may take a few days, but they eventually get done.

Dear Toluwase,

Thanks for the input. I believe that doing it gradually will get you to the finish line faster than applying an HPC-based algorithm and running a massive ab intio simulation.

Best luck,

Wes