This title appears in the Scientific Report :
2016
Please use the identifier:
http://dx.doi.org/10.1002/prot.24939 in citations.
Protein structure refinement with adaptively restrained homologous replicas
Protein structure refinement with adaptively restrained homologous replicas
A novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replic...
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Personal Name(s): | Della Corte, Dennis |
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Wildberg, André / Schröder, Gunnar (Corresponding author) | |
Contributing Institute: |
JARA - HPC; JARA-HPC Strukturbiochemie; ICS-6 |
Published in: | Proteins, 84 (2016) S1, S. 302-313 |
Imprint: |
New York, NY
Wiley-Liss
2016
|
PubMed ID: |
26441154 |
DOI: |
10.1002/prot.24939 |
Document Type: |
Journal Article |
Research Program: |
Critical Assessment of Protein Structure Prediction 11 Functional Macromolecules and Complexes |
Publikationsportal JuSER |
A novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replicas. It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with current state of the art methods. The performance of this protocol in the CASP11 experiment is discussed. We found that the quality of the refined model is correlated with the structural variance of the coupled replicas, which therefore provides a good estimator of model quality. Furthermore, some remarkable refinement results are discussed in detail. |