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Prediction of protein-ligand complex structure by docking software guided by other complex structures
Yoshifumi Fukunishi1, Haruki Nakamura
1Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan. y-fukunishi@jbirc.aist.go.jp
Abstract:
We developed a new scoring method that selects a protein-ligand complex structure with higher geometrical accuracy than the top-scoring complex structure, using the structural information of known protein-ligand complexes. To apply this method, one or more protein-ligand complex structures must be known for the target protein. A number of predicted structures were generated by the protein-compound docking program for a new ligand, and one of these structures, which showed the maximum overlap with the ligand coordinates of the known protein-ligand complex, was selected as the most probable complex structure.
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