Section: New Results

SAM : Spherical Polar Fourier Assembly of Protein Complexes with Arbitrary Point Group Symmetry

Participants : David W. Ritchie, Sergei Grudinin.

We presented a novel FFT-based ab inito docking algorithm called “SAM” for building perfectly symmetrical models of protein complexes with arbitrary point group symmetry. The basic approach uses a novel and very fast 1D symmetry-constrained spherical polar Fourier search to assemble cyclic $C_n$ systems from a given protein monomer. Structures with higher order ($D_n$, $T$, $O$, and $I$) point group symmetries may be built using a subsequent symmetry-constrained Fourier domain search to assemble trimeric sub-units. Our results show that the SAM algorithm can correctly assemble monomers of up to around 500 residues to produce a near-native complex structure with the given point group symmetry in 17 out of 18 test cases. The SAM program may be downloaded for academic use at http://sam.loria.fr/.