Protein-protein complex structure predictions by multimeric threading and template recombination

The total number of protein-protein complex structures currently available in the Protein Data Bank (PDB) is six times smaller than the total number of tertiary structures in the PDB, which limits the power of homology-based approaches to complex structure modeling. We present a threading-recombination approach, COTH, to boost the protein complex structure library by combining tertiary structure templates with complex alignments. The query sequences are first aligned to complex templates using a modified dynamic programming algorithm, guided by ab initio binding-site predictions. The monomer alignments are then shifted to the multimeric template framework by structural alignments. COTH was tested on 500 nonhomologous dimeric proteins, which can successfully detect correct templates for 50% of the cases after homologous templates are excluded, which significantly outperforms conventional homology modeling algorithms. It also shows a higher accuracy in interface modeling than rigid-body docking of unbound structures from ZDOCK although with lower coverage. These data demonstrate new avenues to model complex structures from nonhomologous templates.