DOMpro predicts domain locations using a 1D-RNN. DOMpro takes an input the sequence profile, predicted secondary structure, and predicted relative solvent accessiblity. The output of the 1D-RNN is a classification for each residue as being in a domain boundary region or not. The domains are then infered from this output.
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J. Cheng, M. Sweredoski, & P. Baldi.
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.
Knowledge Discovery and Data Mining, vol. 13, no. 1, pp. 1-20, (2006)