A stepwise docking molecular dynamics approach for simulating antibody recognition with substantial conformational changes

Conformational modifications or rearrangements are frequent occasions throughout inter-biomolecular recognition. Monitoring these modifications are important for exploring the allosteric mechanism and it’s often achieved by molecular dynamics simulation in silico. We beforehand recognized a broad-neutralizing antibody towards H5 influenza virus, 13D4, and solved the crystal constructions of the free 13D4 Fab and its advanced with hemagglutinin…

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