Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38‐45

摘要: We participated in CARPI rounds 38-45 both as a server predictor and human predictor. These CAPRI provided excellent opportunities for testing prediction methods three classes of protein interactions, that is, protein-protein, protein-peptide, protein-oligosaccharide interactions. Both template-based (GalaxyTBM monomer protein, GalaxyHomomer homo-oligomer GalaxyPepDock protein-peptide complex) ab initio docking (GalaxyTongDock GalaxyPPDock oligomer, GalaxyPepDock-ab-initio complex, GalaxyDock2 Galaxy7TM have been tested. Template-based depend heavily on the availability proper templates template-target similarity, difference is responsible inaccuracy models. Inaccurate models could be improved by our structure refinement loop modeling based physics-based energy optimization (GalaxyRefineComplex GalaxyLoop) several targets. Current require accurate structures input. Small conformational changes from input accounted methods, producing one best However, predicting large involving backbone still challenging, full exploration such problems to come.