Standalone Tool-Protein Primary, Secondary & Teritary Prediction

Question

[jackuser1979]

Hi all, Is there any standalone tool which do all primary analysis, secondary structure analysis for a bulk of protein sequence.? (e.g. like protpram -molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity), subcellular localization, signalP & Transmembrane helix prediction, secondary structure prediction, protein function prediction, GO annotation.

Please also let me know any script to automate homology modelling softwares (like submitting sequence one by one) to any of modelling softwares like modeller or I-TASSER?

[shelly.deforte]

I'm pretty sure the all in one solution you're looking for doesn't exist. Protein analysis tools haven't come as far as genome analysis tools. However, all the components you are looking for definitely exist. I would find the best regarded of each tool and create a custom pipeline.

Answer 1

[João Rodrigues]

Hello,

The best you can do to automate things is to install MODELLER locally, since it's extremely easy to script. Otherwise, I doubt that you will make web server developers happy by batch submission of jobs via a script.. if they wanted this functionality they would have made it available (i.e. via a restful interface or something similar).

Most of the things you are asking are useless for tertiary structure modelling. You should narrow down the analysis you want to perform based on your goal. If your goal is to run everything and find out later what to do with it, or hope that is gives something interesting back, you should re-think your project (and approach). In any case, once you find out what you really need, you'll likely find a server/tool that does it all.

As for the analysis. For primary sequence analysis, check the EXPASY server tools, for secondary structure prediction there are plenty of methods, and the same goes for transmembrane segment prediction (usually they come hand in hand). The only page I can think of that condenses MOST of these is the Bioinformatic Toolkit.

Cheers

[shelly.deforte]

"If your goal is to run everything and find out later what to do with it, or hope that is gives something interesting back, you should re-think your project (and approach)"

+1 for this :) I've BTDT.