Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand compl

Background: Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. Results: To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG), CaM kinase kinase (CaMKK) and the plasma membrane Ca2+ ATPase pump (PMCA), and thir...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Nobuyuki Uchikoga, Takatsugu Hirokawa
• Keywords: BMCBI 2010, Interaction Fingerprint, Large Conformational Changes, Protein-protein Interactions