Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry

David W. Ritchie 1 Sergei Grudinin 2
1 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
2 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
Abstract : A novel fast Fourier transform-based ab inito docking algorithm called SAM is presented, for building perfectly symmetrical models of protein complexes with arbitrary point group symmetry. The basic approach uses a novel and very fast one-dimensional symmetry-constrained spherical polar Fourier search to assemble cyclic Cn systems from a given protein monomer. Structures with higher-order (Dn, T, O and I) point group symmetries may be built using a subsequent symmetry-constrained Fourier domain search to assemble trimeric sub-units. The results reported here 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/.
Keywords : symmetry docking point group symmetry protein docking polar Fourier correlation
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David W. Ritchie, Sergei Grudinin. Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry. Journal of Applied Crystallography, International Union of Crystallography, 2016, 49 (1), pp.158-167. ⟨10.1107/S1600576715022931⟩. ⟨hal-01261402⟩

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