PIVOT (Protein Interactions VisualizatiOn Tool) is a Java-based tool, for visualizing protein-protein interactions. It is rich in features that help the users navigate and interpret the interactions map, as well as graph-theory algorithms for easily connecting remote proteins to the displayed map.PIVOT is not limited to the data present in any database, but instead allows the users to create their own dataset, by importing any available lists of interactions and combining them together. PIVOT is currently configured to work with proteins from four different species (human, yeast, drosophila and mouse), and present functional annotations, designations of homologs from the four species, and links to information pages. The protein data is stored in an MS-Access file, easily modifiable by the users to enter their own data.
PESCADOR (Platform for Exploration of Significant Concepts AssociateD to co-Occurrences Relationships) is a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts.
PiType is an accurate 3D structure-independent computational method for classifying protein interactions into simultaneously possible (SP) and mutually exclusive (ME) as well as into obligate and non-obligate.
FlexDock is a fully automated method for flexible docking with large scale motion in one of the docked molecules. The method automatically identifies hinge regions and rigid parts using HingeProt and then docks the input molecules while explicitly considering the hinges and possible protein motions.
InferPPI aims to infer protein-protein interaction based on the parsimony principle of domain-domain interactions. Specifically, inferring domain interactions is a first step and formulated as an integer linear programming with different searching degree of training protein interaction. Then the model is solved by relaxed linear programming. By using the obtained domain interactions, novel protein interactions can be predicted by a formula. In contrast to probabilistic algorithms, InferPPI is an algorithm based on a deterministic model.