3dRPC
Three-dimensional structures of complexes of non-coding RNAs with other biomolecules are urgently needed to understand their diverse newly discovered functions. However, the number of them is very limited at present due to difficulties in experimental measure. To solve this problem, computational prediction is another possible approach.For RNA-protein complexes, some protocolshave been proposed for the prediction of the three-dimensional structures, though with parts of algorithms borrowed directly from those of protein-protein complexes only achieved unsatisfying accuracy as the features of RNA-protein interfaces aresignificantly different from those of protein-protein interface. Therefore, we provide a novel computational protocol for RNA-protein complex structure prediction, which adapts new schemes to discrete molecule and charge and to build reference state in order to include specific features of RNA-protein interface. Benchmark shows that this protocol can achieve a high accuracy comparable to current well-developed algorithms for three-dimensional structure prediction of protein-protein complexes.

If you feel it is useful, please cite:

Huang, Y., et al., A novel protocol for three-dimensional structure prediction of RNA-protein complexes. Sci Rep, 2013. 3: p. 1887.
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