2007. Benchmarking of TASSER in the ab initio limit

ABSTRACT A significant number of protein sequences in a given proteome have no obvious evolutionarily related protein in the database of solved protein structures, the PDB. Under these conditions, ab initio or template-free modeling methods are the sole means of predicting protein structure. To assess its expected performance on proteomes, the TASSER structure prediction algo-rithm is benchmarked in the ab initio limit on a representative set of 1129 nonhomologous sequen-ces ranging from 40 to 200 residues that cover the PDB at 30 % sequence identity and which adopt a, a 1 b, and b secondary structures. For sequences in the 40–100 (100–200) residue range, as assessed by their root mean square deviation from native, RMSD, the best of the top five ranked models of TASSER has a global fold that is significantly close to the native structure for 25 % (16%) of the sequen-ces, and with a correct identification of the struc-ture of the protein core for 59 % (36%). In the absence of a native structure, the structural simi-larity among the top five ranked models is a mod-erately reliable predictor of folding accuracy. If we classify the sequences according to their sec-ondary structure content, then 64 % (36%) of a, 43% (24%) of a 1 b, and 20 % (12%) of b sequences in the 40–100 (100–200) residue range have a significant TM-score (TM-score ‡0.4). TASSER performs best on helical proteins because there are less second-ary structural elements to arrange in a helical protein than in a beta protein of equal length, since the average length of a helix is longer than that of a strand. In addition, helical proteins have shorter loops and dangling tails. If we exclude these flexible fragments, then TASSER has similar accuracy for sequences containing the same num-ber of secondary structural elements, irrespective of whether they are helices and/or strands. Thus, it is the effective configurational entropy of the protein that dictates the average likelihood of cor-rectly arranging the secondary structure elements