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The nomenclature used for describing the individual amino acid residues (P3, P2, P1, P1′, P2′, etc.) of a substrate and the corresponding subsites (S3, S2, S1, S1′, S2′, etc.) of a protease is that of Schechter and Berger: Schechter, I.; Berger, A. On the Size of the Active Site in Proteases. I. Papain. Biochem. Biophys. Res. Commun. 1967, 27, 157-162.
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note
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The structures were minimized in a two-step procedure: (A) using the standard Tripos Force Field without electrostatics applying the Powell minimization technique. The convergence criteria were set to be an energy change of <0.05 kcal/mol in two consecutive steps; (B) the resulting structure was minimized under the same conditions in the protease environment (brook-haven: 4HVP without inhibitor) which was defined as completely rigid. Distance constraints corresponding to a set of hydrogen bonds between inhibitor and protein were applied as described in footnote 11. If the conformation of the modeled structure displayed unfavorable interactions or did not fulfill the distance constrain requirements to a large extent, the starting conformation was manually modified and the new conformer was subjected again to minimization procedures A and B.
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