Algorithm Eisenberg

Profile threading methods As described in Section 6.2, algorithms that optimize threading profiles are the same as for pairwise sequence alignment and are based on dynamic programming. These methods have been introduced by Eisenberg et al. [136, 193, 194]. 

Marcotte, E. M., M. Pellegrini, M. J. Thompson, T. O. Yeates, and D. Eisenberg. 1999. A combined algorithm for genome-wide prediction of protein function. Nature 402 83-6. 

The prediction results for three commonly used prediction methods that of Rao and Argos [20], that of Eisenberg et al. [18], and that of Rost et al. [9] can be compared with our results listed in Table 7 for the data set of 10 best known membrane proteins with observed 717 residues in the membrane-spanning helix conformation (Supplementary Material, Table V). Eisenberg s algorithm overpredicts 5 helices in the subunits M, and L from the photosynthetic reaction center, and has correspondigly low performance parameter for all ten proteins = 0.470 (195 underpredicted and 185 overpredicted residues). Rao and Argos... 

Knepley MG, Karpeev DA, Davidovits S, Eisenberg RS, Gillespie D An efficient algorithm for classical density functional theory in three dimensions ionic solutions, J Chem Phys 132(12) 124101, 2010. 

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