Recommendation of 3D protein structure prediction softwares

Question

[Alec Watanabe]

Hello guys!

I know I can pretty much search for prediction softwares on the Internet, but I want to know your personal opinion and professional experiences with 3D protein prediction softwares. Web-based would be preferable, but standalone is okay. Which software do you recommend? I have a set of proteins that need to have their 3D structure predicted for a posterior docking analysis. Thank you in advance.

Answer 1

[Kevin Blighe]

Please see my suggestions here under 'Protein modelling': A: pathogenicity predictors of cancer mutations

There are numerous algorithms available, all requiring academic / not-for-profit affiliations.

Kevin

[Alec Watanabe]

Thank you. I will read their documentations and check which fulfills my necessities.

Answer 2

[Joe]

The I-TASSER suite and Phyre are among 2 of the best I've used.

SwissModel and MODELLER are also pretty good/extensively used from what I hear, though I've no experience with them personally.

[Alec Watanabe]

Thank you. The software I usually utilize is called MHOLline, but unfortunately it's offline due to maintenance reasons. I'll check the ones you listed,