InSane: Overview



InSane is an acronym for "interactive structure assisted NOE evaluation. The objective of InSane is to automatically assign the NOESY spectrum of the protein in a protein-ligand complex, based on the known structure of the protein in apo form, or in complex with another ligand. After manual assignment of the remaining spectrum, and manual corrections of erroneous automatic assignments, guided by some graphics tools in Wit!P, the assigned spectrum may be converted to an X-Plor distance constraints file and used for the generation of 3D structures in CNX or X-Plor. The InSane assignment method is similar to the SANE [1] procedure developed by the Wright group at the Scripps Research Institute, except that InSane uses raw NOE data in addition to crosspeak lists.

The InSane method is implemented in Wit!P's NMR module (sample script available here.)


Input:

The following files are required for an InSane analysis in Wit!P:

Algorithm:

  1. generate list of pseudoatoms (groups of equivalent protons),
  2. generate list of pseudoatom pairs (up to a very generous 100 Å cutoff),
  3. apply user specified filters to pseudoatom pair list (e.g. NOE intensity, distance),
  4. for each NOE crosspeak: find all potential assignments in the filtered pseudoatom pair list (chem. shifts within user specified tolerance of peak position in all dimensions),
  5. for crosspeaks with ambiguous assignments: reduce ambiguity by eliminating pesudoatom pairs which are judged to contribute only marginally to the observed NOE intensity (based on the known 3D structure of the protein),
  6. write annotated crosspeak list to disk, apply manual corrections, and convert to X-Plor constraints file.

Output:

Annotated crosspeak list in Felix or Sparky format. The perl script xpk2xpl and delxpk may be used to convert annotated Felix crosspeak files to X-Plor distance constraint files.



References:

1. B.M.Duggan, G.B.Legge, H.J.Dyson, P.E.Wright:
SANE (structure assisted NOE evaluation): An automated model-based approach for NOE assignment.
J.Biomol.NMR, 19, 321-329, 2001



A.Widmer, NIBR/CPC/CSG-SB