Automated 2D NOESY assignment and structure calculation of crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs

The NOAH/DIAMOD program suite was used to automatically assign an experimen tal 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using fee dback filtering and self-correcting distance geometry (SECODG). Automatical ly picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calcul ate an ensemble of 40 structures from these NOE distance constraints and ra ndom starting structures. The 10 structures with smallest target function v alues were analyzed by the structure-based filter, NOAH, and a new set of p ossible assignments was automatically generated based on chemical shifts an d distance constraints violations. After 60 iterations and final energy min imization, the 10 structures with smallest target functions converged to 1. 48 Angstrom for backbone atoms. Despite several missing chemical shifts, 42 6 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously a ssigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOA H due to the incomplete proton chemical shifts list. (C) 1999 Academic Pres s.