MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information

We develop a new threading algorithm MUSTER by extending the previous sequence profile-profile alignment method, PPA. It combines various sequence and structure information into single-body terms which can be conveniently used in dynamic programming search: (1) sequence profiles; (2) secondary structures; (3) structure fragment profiles; (4) solvent accessibility; (5) dihedral torsion angles; (6) hydrophobic scoring matrix. The balance of the weighting parameters is optimized by a grading search based on the average TM-score of 111 training proteins which shows a better performance than using the conventional optimization methods based on the PROSUP database. The algorithm is tested on 500 nonhomologous proteins independent of the training sets. After removing the homologous templates with a sequence identity to the target >30%, in 224 cases, the first template alignment has the correct topology with a TM-score >0.5. Even with a more stringent cutoff by removing the templates with a sequence identity >20% or detectable by PSI-BLAST with an E-value 0.5. Dependent on the homology cutoffs, the average TM-score of the first threading alignments by MUSTER is 5.1-6.3% higher than that by PPA. This improvement is statistically significant by the Wilcoxon signed rank test with a P-value < 1.0 x 10(-13), which demonstrates the effect of additional structural information on the protein fold recognition. The MUSTER server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/MUSTER.