A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction

Details A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction

2008-02-21

arxiv.org/abs/0802.3140v1

Biology

Quantitative Biology

Biomolecules

Scientific paper

De novo prediction of protein structures, the prediction of structures from amino-acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we develop a new method of de novo prediction, which combines the fragment assembly method and the simulation of physical folding process: Structures which have consistently assembled fragments are dynamically searched by Langevin molecular dynamics of conformational change. The benchmarking test shows that the prediction is improved when the candidate structures are cross-checked by an empirically derived score function.

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