Summary
Metadynamics MD simulations on CDRH3 dynamics by (1) used a “linear combination of sine and cosine of the psi torsion angles” as Collective variables. This was shown in a previous paper to capture conformational transitions comprehensively. In one study, the CDRL3 loop was also included.
1.
Fernández-Quintero ML, Loeffler JR, Bacher LM, Waibl F, Seidler CA, Liedl KR. Local and Global Rigidification Upon Antibody Affinity Maturation. Frontiers in Molecular Biosciences. 2020;7. Available from: https://doi.org/10.3389/fmolb.2020.00182