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. Author manuscript; available in PMC: 2014 Dec 20.
Published in final edited form as: ACS Synth Biol. 2013 Aug 22;2(12):724–733. doi: 10.1021/sb400076r

Figure 1. Calculating SCHEMA disruption values for virus capsids.

Figure 1

(a) For each chimera considered, SCHEMA was used to calculate the number of residue-residue contacts broken (E) within VP chimeras created by recombining sequence elements from AAV2 (red) and AAV4 (blue). The number of contacts broken (b) within each capsid subunit and (c) between one VP subunit and all contacting subunits (transparent subunits) were used to calculate (d) the number of contacts broken within a fully assembled capsid. The total disruption per subunit (Esubunit) is defined as the sum of Eintra and 0.5·Einter, and the total disruption per capsid (Ecapsid) is calculated as 60·Eintra + 30·Einter. The chimera shown, whose subunits were created using residues 1–474 from AAV4 and 475–734 from AAV2, was mapped onto the AAV4 capsid structure (PDB ID: 2G8G) using Pymol.