I tried using I-TASSER, ROSSETA, and RaptorX but all of these deal with proteins having less that 2000 residues. I am trying to analyze an APC protein which has 2843 amino acids.
Hello Hamed,
I used modbase, I think it gives models which are similar to the proteins in terms of sequence. The first hit I got is of crystal structure of a full-length zebrafish beta-catenin.
So basically it is giving me structures which are similar to my protein APC, am I right?
I thought it will generate structure based on sequence as I-TASSER does.
Sorry I do not know much about Bioinformatics.
modbase is a web interface of MODELLER software.Modeller provides three dimensional structure base on known related structures.(probably in your case zebrafish beta-catenin). anyway I suggest using Modeller instead of modbase.
documentation :
https://salilab.org/modeller/documentation.html
tutorial:
https://salilab.org/modeller/tutorial/
You can try Module 2 of TSPpred webserver (http://crdd.osdd.net/raghava/tsppred/submitseq.html). Its not published yet, but can solve your protein 3D structure with more than 2000 residues.
I used GENO3D and it as given me some structures . I will still try TSPpred webserver and Modeller as well.
Thanks
Hello Sandeep,
I tried TSPpred and it worked I guess. I recieved email with link to the structure but after going to the link it redirected me to the home page. I realised you are one of the developers of TSPpred, so can you send the links to me again or should I again submit the sequence ??
Thanks
Hello Vrushali, can you please give me the Job number of your query. I will then look into it.
Hello Vrushali, It appears you have entered protein sequence in FASTA format. But TSPpred accepts input in only SINGLE LETTER CODE and without any fasta header. Just enter the sequence.
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