iPTMnet aims to provide answers for questions such as: (i) What PTMs of a protein of interest are known? (ii) What specific enzymes (kinases, methylases, etc.) are known to modify a given protein? (iii) What substrates are known for a given PTM enzyme? (iv) What interacting partners are known for each PTM form of a given protein? (v) What protein modifications and enzymes are known in a given signaling pathway? In addition, iPTMnet can be used to generate training sets for PTM site prediction methods.
The specific aims of iPTMnet project are to:
- Develop an integrative bioinformatics framework for PTM discovery, connecting enzyme-substrate relationships, major PTMs that may work in concert, PTM forms to biological contexts and across taxons;
- Develop a bioinformatics resource, iPTMnet, for studying PTM networks in plants with scientific case studies;
- Provide broad dissemination with interoperable resource sharing, training, outreach and integrated education.
The iPTMnet will provide data and tools essential for the understanding of plant PTM networks. A PTM enzyme-substrate database will be developed, combining text mining and data mining results with evidence attribution to capture relevant PTM information and their functional impact, such as interacting proteins, function, pathway, subcellular location, gene expression, protein expression and growth/developmental phenotype. The web portal will allow biologists to search, browse, review results interactively, visualize PTM in protein networks and pathway maps, conduct use cases (such as finding target substrates of given enzymes and vice versa), and capture expert knowledge via community annotation. Scientific case studies will be developed to demonstrate the integrative bioinformatics approach for hypothesis generation, with lab validation of the in silico analysis.