Membrane Proteins (MPs) are biologically and pharmaceutically important. Computational modeling and structure prediction are vital to studies thereof. Accurate model-quality-assessment programs benefit such approaches. Few such programs have been proposed that perform accurately on a broad range of MP classes. We developed a new model-scoring function, Interaction-based Quality assessment (IQ), which analyses inter-residue interactions within the transmembrane domains of helical MPs. Tested using three high-quality model sets: all 206 models of GPCR Dock 2008, all 284 models of GPCR Dock 2010, and all 92 helical MP models of the HOMEP set, IQ selects the native structures from among all of the models with success rates of 93, 85, and 100%, respectively. A recently published model-assessment program for MP structures, ProQM, gave corresponding success rates of 85, 79, and 92%, suggesting that IQ outperforms ProQM when considering only the models' transmembrane regions. IQ should benefit the computational modeling of MPs.

Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions

244th National Meeting (2012)

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