The SDPMOD server performs comparative modeling
in the four steps as follows: (1) template selection, (2) target-template
alignment, (3) model building, and (4) model evaluation.
The detailed procedure for automated modeling is
shown in the flowchart below. The non-redundant template dataset
is first filtered using the number of cysteine, and the resulting
template seqeuences aligned with the target sequence by Stretcher
(a global alignment program which is part of the EMBOSS package)
using a modified scoring matrix derived from the non-redundant SDPs
dataset. The best templates were selected based on the alignment
scores. Target-template alignment and model building were achieved
using a customized matrix to ensure that all the cysteines are well
aligned. The final models were chosen according to the MODELLER
objective function score, which reflects low energy and less violation.
The stereochemical quality of the generated models were evaluated
The flowchart below shows the detailed procedure of the comparative