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:
-
generate list of pseudoatoms (groups
of equivalent protons),
-
generate list of pseudoatom pairs (up to a very generous 100 Å cutoff),
-
apply user specified filters to pseudoatom
pair list (e.g. NOE intensity, distance),
-
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),
-
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),
-
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