: Protein can be classified in different classes. A lot of research is being performed for analyzing the structure and classes of protein. There are many problems associated with protein structure. Some of them are folding problem and protein structure prediction (PSP) etc. PSP is the most considerable open problem in field of biology. In the present work different algorithms like particle swarm optimization (PSO), gravitational search algorithm (GSA) and K-Mean clustering algorithms are used to classify different structures of protein. A random forest (RF) classifier is proposed for analyzing and comparing different protein classes in terms of other conventionally available algorithms in terms of various performance parameters like accuracy, recall, precision and specificity. The proposed classifier proved better than other classifiers in terms of accuracy and can be helpful in predicting the protein structures. A hybrid PSO-GSA algorithm is also proposed which provided improved performance as compared to single algorithms and can be utilized for analysis of protein structure.