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 by MODELLER 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 by PROCHECK. The flowchart below shows the detailed procedure of the comparative modeling process.