In this chapter, we describe a protocol to estimate the thermal stability of single domain antibodies (sdAbs) using molecular dynamics (MD) simulations. This method measures the Q-value, the fraction of the native contacts, along the trajectory of high-temperature MD simulations starting from the experimental X-ray structure. We show a good correlation between the Q-value and the experimental melting temperature (T) in seven sdAbs. Assessing the Q-value on a per-residue level enabled us to identify residues that contribute to the instability and thus demonstrate which residues could be mutated to improve the stability and have later been validated by experiments. Our protocol extends beyond the application on sdAbs, as it is also suitable for other proteins and to determine the interfacial stability between protein and ligand.
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