PiNAT assesses protein protein interaction (PPI) networks and simulates the flow of processes and pathways in the cell. The input to PiNAT a list of protein identifiers. These identifiers are used to query PPI databases, to retrieve all experimentally known interactions, to build a network,and to render this network on the image of a cell according to the predicted localization of the interactions.
Response times are usually larger than minutes because PiNAT queries require heavy CPU usage.
We are currently working on a new release for the pinat software. please forward any questions or comments to assistant at rostlab dot org.
How to use PiNAT
You can submit a list of protein names (UniProt, Swissprot / Trebml, Genbank or DIP) You can also submit your own network.
You should specify the depth of the PPI network around your query proteins. A depth of 1 means that PiNAT will retrieve all the interactions that involve your query proteins. A depth of 2 will retrieve also the interactions that involve proteins of depth 1, and so forth.Output: PiNat returns two types of output:
- a table with the biological reasonabilty of each PPI (Low, Neutral or High), based on two different assessments.
- A schematic representation of the process in the cell. It also returns a GML file that could be downloaded and viewed with cytoscape.