Thus we compared the N-terminal region of the 9 proteins by multiple alignment and secondary structure predictions.
Multiple alignment and secondary structure prediction support the PSI-BLAST results and reveal a classical HTH motif in the COG2886 family.
The multiple alignment and secondary structure prediction suggest that these 9 proteins share one β1- α1- α2- β2- β3 pattern near their N-terminals (Additional file 1, Figure S1), although there were the differences in the length and composition of the predicted secondary structure elements.
Using support vector machines with multiple alignments and secondary structure predictions from PSIPRED [20], Zhang et al. obtained a Matthews correlation coefficient of 0.45, which was slightly higher than the E-SSpred method.
Using multiple alignments and secondary structure predictions, we define the catalytic core of these enzymes to contain a novel α+β scaffold with 6 conserved acidic residues and 4 basic residues.
By comparison of the predicted secondary structure with multiple alignment, most of these secondary structures fall in the conserved region, suggesting that FBG domains have similar domain architectures in the FREP gene family.
In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries.
(M2) Align { x} ∪ D and predict a common secondary structure of the predicted multiple alignment, and then mapped the common secondary structure to the target sequence x.
We computed multiple alignment studies, solvent accessibility calculations, secondary structure analysis, stabilization centers and stabilizing residues before and after the docking process.
Web services at the University of Dundee were created in 2005 as part of the Jalview project (Waterhouse et al., 2009) to provide its users access to ClustalW (Larkin et al., 2007), Mafft (Katoh and Toh, 2008) and Muscle (Edgar, 2004) multiple alignment programs and the JPred secondary structure predictor (Cole et al., 2008).
