Operations Research is probably one of the most successful fields of applied mathematics used in Economics, Physics, Chemistry, almost everywhere onehastoanalyzehugeamountsofdata.Lately,thesetechniqueswereintroducedin biology, especially in the protein analysis area to support biologists. The fast growth of protein data makes operations research an important issue in bioinformatics, a science which lays on the border between computer science and biology. This paper gives a short overview of the operations research techniques currently used to support structural and functional analysis of proteins. Key words: Protein structure, hidden Markov model, clustering, neural networks, dynamic programming