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. 2013 Sep 12;4:268. doi: 10.3389/fimmu.2013.00268

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Copyright © 2013 Zoete, Irving, Ferber, Cuendet and Michielin.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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(A) The thermodynamic cycle underlying Eq. (1). (B) The dual topology scheme used to interpolate the potential energy function between the Pro side-chain (green) and the Ala side-chain (blue). Common atoms are unaffected, Duplicated atoms change type and non-bonded parameters. Unique atoms vanish, with their non-bonded interactions switched to zero and their bonded interactions unchanged. (C) Derivatives of the free energy obtained for each λ-value in three independent runs for the bound complex. (D) Idem for the unbound complex.