Structure Prediction for protein
When i post Target amino acid sequence in protein structure prediction server II,I'm not getting template structure. Can anyone help with this? I don't know what is the mistake
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ashamscsoft •
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Does finding a homologous usable template not depend on the target sequence and how well it matches existing sequences with known structures?
If you gave us the target sequence, along with details on the target protein as well as what you think the reason might be, you could start a discussion - that would show you've put some thought into this.
When you ask a question summarily as you've done here (with no details and no indication of what you have tried on your part), all the onus is on the person trying to answer, and that is not conducive to discussion.
k I have tried with ataxin-1 taken from uniprot and mutated that sequence, and kept that sequence as my target sequence. Now to get my template structure, I chose protein structure prediction server II. When i give my target sequence i get this error, i will attach the file here. If u want i can attach the target seq also.
Target seq MKSNQERSNECLPPKKREIPATSRSSEEKAPTLPSDNHRVEGTAWLPGNPGGRGHGGGRH GPAGTSVELGLQQGIGLHKALSTGLDYSPPSAPRSVPVATTLPAAYATPQPGTPVSPVQY AHLPHTFQFIGSSQYSGTYASFIPSQLIPPTANPVTSAVASAAGATTPSQRSQLEAYSTL LANMGSLSQTPGHKAEQQQQQQQQQQQQHQHQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ HLSRAPGLITPGSPPPAQQNQYVHISSSPQNTGRTASPPAIPVHLHPHQTMIPHTLTLGP PSQVVMQYADSGSHFVPREATKKAESSRLQQAIQAKEVLNGEMEKSRRYGAPSSADLGLG KAGGKSVPHPYESRHVVVHPSPSDYSSRDPSGVRASVMVLPNSNTPAADLEVQQATHREA SPSTLNDKSGLHLGKPGHRSYALSPHTVIQTTHSASEPLPVGLPATAFYAGTQPPVIGYL SGQQQAITYAGSLPQHLVIPGTQPLLIPVGSTDMEASGAAPAIVTSSPQFAAVPHTFVTT ALPKSENFNPEALVTQAAYPAMVQAQIHLPVVQSVASPAAAPPTLPPYFMKGSIIQLANG ELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVL VEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLKNLKNGSVKKGQPVDPAS VLLKHSKADGLAGSRHRYAEQENGINQGSAQMLSENGELKFPEKMGLPAAPFLTKIEPSK PAATRKRRWSAPESRKLEKSEDEPPLTLPKPSLIPQEVKICIEGRSNVGK
i cannot attach the error file here
Please edit your question and add this information in there. Once done, delete your comment so all the necessary information is in the main post.
I don't see any error. I used this server: http://ps2v3.life.nctu.edu.tw/ because the v2 server seemed to have some PHP/CSS issues processing its output.
How to solve that issue?
I don't think users can solve the issue. You could probably send an email to the developers.
Can u specify anyother reliable tool in online to perform prediction. I know I-Tasser is reliable but it takes 2 or 3 days for predicting 1 sample. So please can u specify anyother reliable tool
I am not a structural biologist, so I don't really know. Also, if you read my comment again, you will notice I provided a possibly acceptable alternative to the tool - a different version of the same tool.
thanks i'm getting in that server. I have another doubt is that possible to induce mutation in protein structure when the mutation information is avaliable for amino acid sequence?
Like I said, I am not a structural biologist. If you have another question, open another thread. Also, please give some thought to the question - especially on what you might mean by "induce mutation in protein structure" - as far as I know, there is no such thing as a structure-level mutation.