The prediction of protein tertiary structure from primary structure remains a challenging task. A possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, we further improve the efficiency of basin-hopping by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. We term this approach secondary-to-tertiary basin-hopping and benchmark it for three miniproteins, trpzip, trp-cage and ER-10. For each of the the three miniproteins the secondaryto-tertiary basin-hopping approach successfully and reliably predicts the three-dimensional structure.When it is applied to larger proteins we also obtain correctly folded structures. We thus conclude that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.1 These authors contributed equally to this work.
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