Kinked CDR H3-like loops are common

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The difficulty of de novo CDR H3 loop modeling is surprising in many cases because of the modest loop lengths at which they occur. One possible explanation is that V(D)J recombination can produce loops that access conformations that are extremely rare in existing protein structural databases. An alternate hypothesis is that the environment formed by the VH and VL domains stabilizes CDR H3 loop conformations that existing methods do not detect as favorable. We identified a diverse set of loops across a wide range of lengths that adopt H3-like conformations. These loops show that the kinked conformation of CDR H3 loops is common.