DOCK 6: combining techniques to model RNA-small molecule complexes.

@article{Lang2009DOCK6C,
  title={DOCK 6: combining techniques to model RNA-small molecule complexes.},
  author={P. Therese Lang and Scott R. Brozell and Sudipto Mukherjee and Eric F. Pettersen and Elaine C. Meng and Veena L. Thomas and Robert C. Rizzo and David A. Case and Thomas L. James and Irwin D. Kuntz},
  journal={RNA},
  year={2009},
  volume={15 6},
  pages={
          1219-30
        }
}
With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design, particularly DOCKing algorithms, to be extended or adapted for nucleic acids. Here, we have compiled a test set of RNA-ligand complexes to validate the ability of the DOCK suite of programs to successfully recreate experimentally determined binding poses. With the optimized parameters and a minimal scoring function, 70% of the test set with… 

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