i want to predict the 3d (tertiary) structure of a hypothetical protein without using homology modeling. suggest me any softwere/online tool that i can use to determine the 3d structure of an unknown,hypotheticl protein & that doesn't depend on homology modeling. thanks in advance.
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Ehsan •
Dear,
Your key term here is ab initio modeling. There is one package available called rosetta (https://www.rosettacommons.org/). Some other programs wills first use homology modeling for parts of the protein that already exists in their database, and then use ab initio to model those parts that do not match. You can check I-TASSER (http://zhanglab.ccmb.med.umich.edu/I-TASSER/). These are just a few examples,
Regards,
Also: check ab initio fold recognition and/or threading based tools: https://en.wikipedia.org/wiki/Threading_(protein_sequence)
Pymol can do modeling, not whole protein but peptides.
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