Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, sheet and coil? I searched but could not find any. There are servers that take in 1 sequence. I want to get the structure of multiple sequences together...
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1$\begingroup$ Why do you want multiple sequences together? What is the problem with doing one after the other? Is there any additional aspect to this that is not evident in the question? $\endgroup$– WYSIWYGCommented Feb 26, 2016 at 6:21
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$\begingroup$ the number of proteins is huge, so I wanted to know if there is any website that allowed batch processing $\endgroup$– girl101Commented Feb 26, 2016 at 6:25
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1$\begingroup$ I am sure some API would exist. What is the server that you are using? Did you check its manual? You can also write a script that can do one-by-one submissions and retrieval. $\endgroup$– WYSIWYGCommented Feb 26, 2016 at 6:27
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$\begingroup$ Also when you have lots of data you should get program not waste time with server. $\endgroup$– MithoronCommented Mar 27, 2016 at 22:02
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$\begingroup$ @Mithoron with this kind of data and computation, that's easier said than done $\endgroup$– MaljamCommented Apr 8, 2016 at 15:28
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2 Answers
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Unfortunately it is impossible to predict the tertiary structure of proteins using raw amino acid sequence. The information required to be computed in the construction of the dynamic protein shape is too large for any computer at the moment.
There are actually a list of research facilities that are looking for people to donate their computer's idle CPU time to help sequence proteins.
Here is a list: (http://www.hyper.net/dc-howto.html).
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$\begingroup$ I really am not concerned about who wants idle computers right now. I need to know if such a server exists or not $\endgroup$– girl101Commented Feb 26, 2016 at 5:26
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$\begingroup$ People are working on it. So no, they don't. $\endgroup$– user22087Commented Feb 26, 2016 at 12:36
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1$\begingroup$ In other words, what OP should be looking for are protein databases that can be indexed with amino acid or DNA sequences. $\endgroup$ Commented Mar 27, 2016 at 7:52
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$\begingroup$ It can't be done exactly but such servers do it more or less accurately, OP wasn't asking if protein folding problem was suddenly resolved. $\endgroup$– MithoronCommented Apr 8, 2016 at 15:34
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If you are only looking for secondary structure prediction you could try the JPred-server API.
On their website they refer to a script that
provides a JPred user with advanced functionality for an easy submission of hundreds of JPred jobs in a sustainable manner. […] For full details on the code, how-to, and for download please check Fabian's GitHub repository page.
