Using evolutionary couplings to optimize dimer prediction with Rosetta SymDock

We present an algorithm EcSymDock which optimized SymDock using Evolution couplings for better performance. SymDock is a protocol of Rosetta used to predict protein oligomer structure. Evolution Coupling (EC) is an optimized mutual information calculated by specific protein family MSA, it reveals certain contacts between residues. Today more and more researchers pay close attention to how to use ECs as constraints during protein structure prediction. We combined EC information with SymDock protocol and present the EcSymDock method to add EC as constraints into SymDock protocol. Testing on a list of dimers shows the method recovers the native dimeric configuration with better accuracy than SymDock and produces many decoys near the native structure in top 400 lowest energy.