STEREOSEARCH

Nilges, M., Clore, G.M., & Gronenborn, A.M. (1990) 1H-NMR Stereospecific Assignments by Conformational Database Searches, Biopolymers 29, 813-822 pubmed

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stereosearch

The program STEREOSEARCH searches a database containing torsion angles, coupling constants and interproton distances to find conformations that satisfy constraints derived from NMR experiments. The search is performed for both possible stereospecific assignments at a prochiral group; by
comparing the results of both searches one can determine the correct assignment. Additionally, torsion angle restraints can be obtained.

The program asks for three files:

1) (OUTPUT) the file containing the results of the search
2) (INPUT) the file containing the constraints derived from
NMR experiments
3) (INPUT) the database file containing the three torsion
angles phi, psi and chi1, and corresponding coupling
constants and interproton distances.


The constraints input file has the following form:

residue ser 23
daN- = 3.5 0.3
dNN+ > dNN- 0.5
..... . ..... ...
..... . ..... ...
JNa = 6.0 2.0
Jab2 = ... ...
Jab3 < ... ...
phi = -60.0 40.0 1
psi = -60.0 40.0 1
chi1 = 60.0 20.0 3
end

Each record has a maximum of five entries:
(1) A connectivity, coupling constant or dihedral angle
(2) A relational operator (>, =, <)
(3) Another connectivity etc. or an absolute value
(4) An error estimate (optional, default is 0). The error estimate can be set to a negative value, then it represents
an offset (thus it is possible to include conditional statements
that one distance has to be larger than the other by at least
some value).
(5) A multiplicity for the angle constraints (optional, default is 0).

For angle constraints the multiplicity should be set at least to 1
(one value per cycle).

The format within the records is free. The constraints can be entered in any order; it may save some CPU time if one enters the most restrictive constraints first.

Connectivities and coupling constants have unique names generated as
follows:
(1) type of constraint:
d connectivity
J coupling constant
(2) first atom type:
a, b2, b3, N for HCa, HCb2, HCb3, HN, resp.
(3) second atom type:
(4) a minus sign for a (i-1,i) connectivity, a plus sign for (i,i+1)
Thus, db2N+ or dNb2+ is the noe connectivity from Hb2 of residue
i to HN of i+1.
Cases are distinguished in the above examples for clarity only; the
program is not case sensitive, everything can be entered uppercase
or lowercase.


The database file is an unformatted file with one record for each conformation. Each record contains the three torsion angles, the associated coupling constants and interproton distances in the following order:

0 NOT USED
1 PHI
2 PSI
3 CHI1
4 JNA
5 JAB2
6 JAB3
7 DAN- 1)
8 DNN- 1)
9 DAB3
10 DAB2
11 DNB3
12 DNB2
13 DNB3+
14 DNB2+
15 DAN
16 DAN+
17 DNN+

(1) As these distances do not depend on phi, psi or chi1, the constraints are not usually used by the search program. They may be useful, though, in connection with a database generated from crystal structures.



 

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last updated: August 2001