Applications of SnB to Proteins1

Russ Miller and Charles M. Weeks
Hauptman-Woodward Medical Research Institute
(716) 856-9600; miller@hwi.buffalo.edu

SnB is a publicly available direct methods software program based on the Shake-and-Bake method of structure determination. It has been used to solve structures containing as many as 600 nonhydrogen atoms, given data to 1.1Å. This ab initio procedure consists of cyclically processing random structures through a series of phase refinement and Fourier refinement steps in an effort to reduce the value of Hauptman's minimal function.

StructureNonhydrogen AtomsSpace GroupResolutionSuccess Rate2
Er-1 pheromone3302C21.00Å1.5%
Gramicidin A 317 P212121 0.86Å 0.3%
Crambin 400 P21 0.83Å 4.0%
Alpha-1 peptide4 450 P1 0.93Å 5.0%
Rubredoxin 500 P21 0.92Å 3.0%
ToxII 620 P212121 0.96Å 1/1619
In addition, SnB has also been used to solve numerous previously unknown structures in the 100-200 nonhydrogen atom range, some of which could not be solved by traditional tangent-based direct methods.

Computing platforms for SnB include Unix workstations, the TMC CM-5, the Cray C90, the Cray T3D, and the IBM SP2. It is available at several of the NSF supercomputing centers and has been incorporated into Molecular Structure Corporation's teXsan package, vers. 1.7-3.

1This research was supported by NIH grant GM-46733 and NSF grant IRI9412415.
2Percentage of randomly generated trial structures that go to solution.
3Structure initially solved by SnB: Anderson et al., Abs. ACA (23), 4a.7.A, p. 80.
4Structure initially solved by SnB: Prive et al., Abs. ACA (23), W008, p. 149.