This title appears in the Scientific Report :
2014
Please use the identifier:
http://dx.doi.org/10.1002/cphc.201402247 in citations.
Protein Structure Prediction: Assembly of Secondary Structure Elements by Basin-Hopping
Protein Structure Prediction: Assembly of Secondary Structure Elements by Basin-Hopping
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 introducin...
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Personal Name(s): | Hoffmann, Falk |
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Vancea, Ioan / Kamat, Sanjay G. / Strodel, Birgit (Corresponding Author) | |
Contributing Institute: |
Strukturbiochemie; ICS-6 |
Published in: | ChemPhysChem, 15 (2014) 15, S. 3378–3390 |
Imprint: |
Weinheim
Wiley-VCH Verl.
2014
|
PubMed ID: |
25056272 |
DOI: |
10.1002/cphc.201402247 |
Document Type: |
Journal Article |
Research Program: |
Structural Biology |
Publikationsportal JuSER |
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. |