An integrated methodology is proposed to combine the major areas of protein analysis. It can be considered as a guideline that can be used to analyze and model a protein. This methodology is applied on one of proteins' viruses for analysis and modeling; non-structural protein 5a (NS5a) of Hepatitis C virus (HCV). Also, SemiBoost-Fold Recognition (SB-FR) algorithm is proposed for predicting protein fold. SB-FR proposes a semi-supervised boosting combination to achieve better multi-class classification model. A famous challengeable dataset (Ding and Dubchak dataset) is used for training and...