title: Protein structure prediction: assembly of secondary structure elements by basin-hopping.
abstract: The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.
authors: Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany).
authors: Falk
authors: F
authors: Hoffmann
authors: Ioan
authors: I
authors: Vancea
authors: Sanjay G
authors: SG
authors: Kamat
authors: Birgit
authors: B
authors: Strodel
mesh_terms: D000595:Amino Acid Sequence; D008840:Microfilament Proteins / Q000737:chemistry; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D008840:Microfilament Proteins; D011506:Proteins; C026615:villin
keywords: Monte Carlo moves; basin-hopping; molecular modeling; protein structure prediction; secondary structure assembly