Among free software/web servers, Modeller and SwissModel are well regarded.

I have used the commercial software YASARA-Structure and obtained excellent results.

The following softwares were commercially available for Drug discovery approaches.

MOE - www.chemcomp.com/journal/homology.htm

PRIME- https://www.schrodinger.com/prime

BIOVIA- http://www.3dsbiovia.com/services/training/life-science/protein-homology-modeling.html

Homology modeling in YASARA - www.yasara.org/homologymodeling.htm

Among free software/web servers, Modeller and SwissModel are well regarded.

I have used the commercial software YASARA-Structure and obtained excellent results.

The principles of homology modeling do not depend on whether you work with bacterial, plant or human proteins. This may influence the availability of suitable modeling templates, but not the principles of protein folding or the methods used for modeling their structure.

The big integrated software packages are usually directed at the pharma industry and can be very expensive. They usually pack everything related to drug design into one big package, homology modelling, drug design, docking, QSAR, but are often not very transparent as to the exact methods used. I have used MOE for a while, but while I quite liked it, on the long run, it was to pricey, even for an academic lab. The Maestro suite by Schrödinger (https://www.schrodinger.com/maestro) also includes homology modeling.

Please be aware that the best method used for modeling very much depends on the degree of homology to the best templates available, to some extent also on the purpose of the model and the flexibility of the target protein. The CASP contest (critical assessment of methods of protein structure prediction) critically evaluates the power of the different prediction methods:

Article Critical Assessment of Methods of Protein Structure Predicti...

Yasara, Swiss Model in conjunction with the Swiss-PDBViewer (DeepView, https://spdbv.vital-it.ch) and Modeller (https://salilab.org/modeller/) in conjunction with UCSF chimera (https://www.cgl.ucsf.edu/chimera/) are all good choices for modeling projects where good homology templates are available. They all depend on being able to generate a correct sequence alignment.

Threading algorithms such as those used by iTasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) extend homology predictions into the gray zone where the sequence-to-sequence alignment yields unclear results, and where no template with discernible homology is available, ab-initio folding algorithms, e.g. Robetta (http://robetta.bakerlab.org) are used.

Hi SAMEE ULLAH ,

Among the free tools, I have found MODELLER to give me the best results, it is resource intensive, but so are the other standalone tools.

I have personally used YASARA Structure and hands down I can say it gives you one of the best experience to work with, their support is also pretty good as the developer himself helps you with everything.

As long as you have a good template with good amount of sequence similarity, you will get very good reliable homology models through both MODELLER and YASARA structure.

Best,

Arijit

Hi,

Homology modelling can be done using: MODELLER, SWISS-MODEL, Phyre, Phyre2, Psi-Pred.

I have used these tools for my own research work and I will recommend these without any second opinion.

I wish you luck!

Best regards,

Thanks!!! to all especially @Annemarie Honegge appreciate your thoughtful info. I have used MOE-2015 but i think i should try Schrodinger 2018-1.

Prime

A powerful and innovative package for accurate protein structure predictions

https://www.schrodinger.com/prime

Kiran Lokhande Thank you for suggestion

What do you mean by reliable?