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Mutations in homologous proteins affect changes in the backbone conformation that involve a complex interplay of forces which are difficult to predict. Protein design algorithms need to anticipate these backbone changes in order to accurately calculate the energy of the structure given an amino acid sequence, without knowledge of the final, designed sequence. This is related to the problem of predicting small changes in the backbone between highly similar sequences.

Protein backbone ensemble generation explores the local structural space of unseen natural homologs