PlasmoID: A P. falciparum Information Discovery Tool

Abstract

Plasmodium falciparum is the parasite responsible for more than 90% of deaths that occur due to malaria. Organization and mining of 'omic' (genomic, proteomic, transcriptomic, interactomic) data can improve our understanding of P. falciparum biology and help in the fight against malaria. PlasmoID (Plasmodium Information Discovery) is a tool developed for the dynamic exploration of the parasite's 'omic' landscape. Diverse computational and curated P. falciparum protein-protein interaction datasets, as well as binary relationships involving protein-small molecule entities, manually curated protein-protein relationships derived from the published literature and protein-protein interactions based on metabolic pathways are included in the PlasmoID database. The graphical user interface is designed as a plug-in to Cytoscape, an open-source network visualization tool. Important features of this plug-in include a synchronized tabular representation of any network loaded on the canvas, ability to find the shortest path between a pair of nodes in the database, search and expansion of entities from the database, and the ability to add new entities to the database through the interface. Malaria researchers can now seamlessly interrogate heterogeneous 'omic' datasets as well as add proprietary data to generate and visualize P. falciparum pathway and cell process network models. PlasmoID can be downloaded from http://pfalciparum.atc.tcs.com/PlasmoID.

UnderstandingLeishmaniaparasites through proteomics and implications for the clinic

“…Therefore, the analysis requires an understanding of the protein networks and their importance in the biological system. Understanding the topological metrics using an in silico approach has further paved the way for exploring proteins in detail with the help of software such as PSIMAP [157] and PlasmoID [158]. A similar protein interaction and network studies have been reported for L. major using an in silico approach with iPfam, PEIMAP and PSIMAP [159].…”

Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection

“…These studies have also expanded to organisms of medical importance, such as the protozoan parasite Plasmodium falciparum [ 20 ], in the interest of discovering new drug and vaccine targets. This data is available through the system PlasmoID [ 21 ]. Topological analysis has also been useful in detecting important proteins, even when the protein network has been predicted using an orthology-based method, as in the case of the human interactome[ 22 ].…”

A Chemical Proteomics Approach for the Search of Pharmacological Targets of the Antimalarial Clinical Candidate Albitiazolium in Plasmodium falciparum Using Photocrosslinking and Click Chemistry

“…Amino acid sequences of conserved Plasmodium proteins of unknown function were also analyzed in OrthoMCL-DB [47] . Clusters and protein interaction networks were built in Cytoscape 2.5.1 [48] using the PlasmoID database [49] , which integrates data from different experimental and computational resources, including LaCount DJ [23] and PlasmoMAP [24] datasets. The GO Term Finder tool [50] was used at the web interface http://go.princeton.edu/cgi-bin/GOTermFinder to identify ontology terms significantly enriched among the putative albitiazolium targets.…”