Abstract
We present a coarse-grained scoring energy able to identify near-native transmembrane (TM) helices pairs of an ensemble generated by two different strategies: Rigid Body Monte Carlo simulations and a collision detection algorithm (Seetharaman et al., work in progress). We test the scoring energy on a set of four known native transmembrane helix pairs. Near native structures are identified with Cα root mean squared deviation (RMSD) lower than 3 Å. This empirical energy function is based on a knowledge based potential obtained from a representative set of globular protein structures.
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