Perform protein sequence to structure alignments to a library.
Highlights:
Submitted sequences are aligned to each of about 7000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms.
The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure.
A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.
The submitted sequence must be more than 20 and less than 1000 amino acid residues.
The calculation will be run with default gap and insertion penalties.
