Consensus alignment server for reliable comparative modeling with distant templates

J. C. Prasad, S. Vajda, C. J. Camacho
2004 Nucleic Acids Research  
Consensus is a server developed to produce highquality 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 alignment 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
more » ... redictions are typically within 3 Å rms deviations from the crystal structure. Users can upload a target protein 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 homologous protein structure pairs. The Consensus server should prove useful for modelers for whom the structural reliability of the model is critical in their applications. It is currently available at
doi:10.1093/nar/gkh456 pmid:15215349 pmcid:PMC441594 fatcat:2ta6pxrtj5dhnmzwusuxpe2ave