Modeling Large protein structure composed of more that 1000 amino acids with no similarity, or rather similarity score is not significant for homologous proteins which are used as templates.
Parth Sarthi Sen Gupta
I think you can use salilab modeller. In their tutorial they describe different modelling for your large and dissimilar sequence.
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Alexey Nikitin
Good question. For 1000 amino acids we can do a short optimization. It seems that on this simulation ends.
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