Ab-Intio Prediction Of Proteins

Question

[Payal]

Hi friends!

Could nyone tel me which one is the best tool to do ab-intio prediction of proteins?

[Neilfws]

"Prediction of proteins" makes no sense. I assume you mean prediction of protein structure. Also, please improve your spelling.

[Larry_Parnell]

Are you looking for help in predicting protein-coding regions from gene/genomic DNA sequence, or in predicting protein secondary and tertiary structure? Please clarify.

Answer 1

[Rahul]

I-TASSER one of the most reliable server to predict the 3d structure of protein. It uses threading and ab-intio methods to predict the structure.

Answer 2

[Chris Evelo]

I think the answer is "your brain". Seriously, ab-initio predictions are OK if you want to find major structural components like alpha-helixes and beta-sheets. To predict the folds is hard, and human assistance helps. That is why projects like [?]foldit[?] exist. Foldit is available as game and a number of papers with results from the game have been published. See the linked page for those.

[Keith Callenberg]

This is definitely a good point, and the OP and others probably do need to hear it, but the OP didn't ask, "what should I use for structure prediction?" He came here specifically asking for names of good tools for the task. Your comment would have been more constructive if you'd pointed him to the standalone version of foldit: http://depts.washington.edu/uwc4c/express-licenses/assets/foldit/

[Chris Evelo]

Since you seem to want to take this literally, I don't agree. he didn't ask for a list of tools. He asked for the best tool. And my idea about the best tool is indeed "your brain". I assumed that you can find links to the standalone version of foldit on the page I linked though. Thanks for adding that.

Answer 3

[Khader Shameer]

Depending on the length of your protein sequence you may try ab-intio structure prediction using Robetta Server. Manuscript here, also read FAQ before the submission.

Answer 4

[João Rodrigues]

Protein structure prediction is assessed in the CASP (Critical Assessment of protein Structure Prediction) experiment. Instead of going through all the published papers that argue their method/server is the best in this or that category and sometimes give quite confusing metrics to justify it, try checking the list CASP provides as the "best public servers". I-TASSER is there, as is Robetta, but also others like HHPred.

Answer 5

[Reyhaneh]

if you are talking about protein-protein complex prediction (docking) ZDock-Zrank is a state of art ab initio docking and scoring tool.

Answer 6

[Manu Prestat]

If you're talking about ab initio CDS prediction, I would advise you to use GenMark. By the way, this software proposes on-the-fly protein translation if this is what you want.