Tool Description Reference
SMART A Simple Modular Architecture Retrieval Tool; describes multiple information about the protein query. [145]
AutoDock Predicts protein-ligand interaction and is considered as reliable tool. [146]
HADDOCK Describes the modelling and interaction of bio-molecular complexes such as protein-protein, protein-DNA [83]
BIND A database that provides access to molecular interaction and bio-complexes [89]
MOE An integrated package of tools used for drug discovery. It combines visualization, modelling, and drug discovery on one plate-form. [147]
STRING A database of both known and predicted protein interactions. [148]
MIMO A dynamics graph-matching tool for the comparison of biological pathways in an efficient manner. [149]
IntAct It is an open source database system and provides analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. [55]
Graemlin It is capable of scalable multiple network alignment with its functional evolution model that allows both the generalization of existing alignment scoring schemes and the location of conserved network topologies other than protein complexes and metabolic pathways. [150]
PathBLAST It is meant to search protein-protein interaction network of the any selected organism and extracts all interaction pathways that align with the query. [151]
CFinder This tool is capable of finding and visualizing the overlapping dense groups of nodes in networks, and quantitative description of the evolution of social groups. Itis efficient for clustering data represented by genetic or social networks and microarray. [152]
MCODE It is suited for both computationally and biologically oriented researchers. Its features include; Fast network clustering, Fine-tuning of results with numerous node-scoring and cluster-finding parameters, Interactive cluster boundary and content exploration, Multiple result set management, Cluster sub-network creation and plain text export [153]
Table 5: Selected tools to study the molecular interactions.