Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res

Consensus is a server developed to produce high-quality alignments for comparative modeling, and to identify the alignment regions reliable for copying from a given template. This is accomplished even when target–template sequence identity is as low as 5%. Combining the output from five different align-ment methods, the server produces a consensus alignment, with a reliability measure indicated for each position and a prediction of the regions suitable for modeling. Models built using the server predic-tions are typically within 3 A ̊ rms deviations from thecrystalstructure.Users canuploadatargetprotein sequence and specify a template (PDB code); if no template is given, the server will search for one. The method has been validated on a large set of homolo-gous protein structure pairs. The Consensus server should prove useful for modelers for whom the struc-tural reliability of the model is critical in their applica-tions. It is currently available a