Abstract: Guessing the boundaries of structural domains has been an important and challenging problem in experimentand computational structural biology. A promising method for detecting the domain structure of a protein from sequence information alone was presented. The method is based on analyzing multiple sequence alignments that are derived from a database search. Multiple measures were defined to quantify the domain information content of each position along the sequence and were combined into a single predictor using support vector machines. The overall accuracy of the method for a single protein chains dataset is about 85%. The result demonstrates that the utility of the method can help not only predict the complete 3D structure of a protein but also study proteins’ building blocks of functional analysis.

Key words: protein domains, sequence, support vector machine, bi oinformatics