Asparagine linked glycosylation (N-glycosylation) is one of the most predominant posttranslational modification found in eukaryotic proteins and this type of modification has also been found in prokaryotic proteins.The modification is known to be essential for folding, oligomerization, quality control, sorting, and the transport of especially secretory proteins.The modification is carried out by oligosaccharyltransferase (OST) embedded in the membrane of the endoplasmic reticulum.OST translocates a glycan moiety (mainly GlcNAc) to a nitrogen atom in the side chain of an asparagine residue located in an amino acid sequence Asn-Xxx-Thr/Ser, but it is widely accepted that this sequence motif is just a necessary condition for N-glycosylation site.There are many sequences with the motif that have no experimental evidence to be N-glycosylated.A number of computational methods have been developed for narrowing down the target regions for N-glycosylation, but so far there is no method with sufficient reliability comparable to the result of large-scale experimental detection.For this reason, we have made the efforts to develop a new method that will have accuracy comparable to the experimental detection.Our new method incorporated not only position specific score matrices derived from known N-glycosylation sites, but also amino acid constraints derived from a predicted docking structure of a glycosylated peptide and OST.The docking model suggested conformational restrictions of the bound peptide on its side chain volume, dihedral angle, hydrogen-bonding capacity, and so forth.These restraints indirectly limit the variety of amino acid types in a position and in a position pairs near the N-glycosylation sites.By including these features, our prediction turned to have better specificity.Our new method is applied to the proteome of a specific cell and the distribution of the N-glycosylation sites was compared with the experimental results.