If you want to perform de novo modelling, in my opinipon the best option is using Rosetta. If you only want to model mutants from existing proteins, other option is to use some homology modelling software. Starting from the fasta sequence you construct 3D models. I strongly recommend yo the SwissModel server.

Please find the link to my PhD thesis: https://www.escholar.manchester.ac.uk/api/datastream?publicationPid=uk-ac-man-scw:180878&datastreamId=FULL-TEXT.PDF

There, I gave briefly all available softwares and methods for building of proteins and RNAs, as well as softwares in use to check of the quality of the constructed protein in sillico.

Hopefully, it will be helpful for you.

Thanks Arsic!

let me just reframe my question. By chimeric protein I mean a protein which is constructed by linking two or more proteins through some effecter sequences. 

Kusum, they are proteins, so the same modelling strategy you can use to construct with some necessary modifications. 

Hello Kusum,

I was wondering if you have made any progress.  I asked a similar question, here is the link in case any of the information offered to me may be helpful to you.

https://www.researchgate.net/post/I_have_a_chimera_that_I_would_like_to_run_through_a_de_novo_prediction_solution_Which_would_be_best/1

Hi Kusum, you can have a look on

http://www.ncbi.nlm.nih.gov/pubmed/21229277

http://www.ncbi.nlm.nih.gov/pubmed/19799841

These papers uses the approaches to construct chimeric vaccines using in-silico approach.