Prediction of protein-ligand complex structure by docking software guided by other complex structures.
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.
Fukunishi
Yoshifumi
Y
Biological 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
Nakamura
Haruki
H
D001665:Binding Sites; D008024:Ligands; D011237:Predictive Value of Tests; D011485:Protein Binding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D013816:Thermodynamics
D008024:Ligands; D011506:Proteins