Authentication is not mandatory to access the website contents. It is possible to explore all data without authentication. However, to contribute to the compound section, it is necessary to have an account for traceability and recognition purposes.
Yes, you can upload compounds after creating a user account. Refer to the tutorial titled "Tutorial for iPPI-DB website - Contribution mode" in the tutorials section of the IPPIDB website for guidance.
No, it's not possible. However, you can use our other application Indeep <a href="https://indeep-net.gpu.pasteur.cloud/">InDeep-Net</a> .
To search for a complex in the PIE server, you have multiple options available. You can search by entering specific criteria such as protein, ligand, organism, or PDB codes. Additionally, you can navigate through the Protein-Protein Interaction (PPI) pocketome using a minimum spanning tree approach, also known as TMAP. For detailed instructions, please consult the tutorial titled "Tutorial for Query mode" found in the tutorials section of the IPPIDB website.
PIE, short for Protein Interaction Explorer, is a component of IPPIDB designed to integrate various visualization tools aimed at exploring and analyzing protein interactions. PIE offers features such as the integration of detected pockets through the program VolSite, predictions of functional binding sites from our tool InDeep, calculation of hot spots using the program FoldX, overlaying liganded protein chains onto their corresponding heterodimer complex, and a pocket similarity metric to hypothesize possible partner repurposing.
PIE is part of the IPPI-DB platform and can be accessed via the top panel of the IPPI-DB website. It is a recent add-on that exclusively focuses on the structural data of the PDB related to protein-protein interaction.
No, it is not possible to upload new data to PIE. However, PIE is regularly updated each year to incorporate new structural data automatically.
No, the data and tools of PIE can be accessed without any authentication.
The term "pocketome" refers to the complete set of protein-protein interaction binding pockets stored on the PIE server. The pocketome visualization on PIE enables exploration and analysis of protein-protein interaction pockets either by clicking on each pocket or utilizing the search field.
TMAP, or TreeMap, is an innovative interactive visualization tool designed to showcase all the pockets extracted from various protein structures stored on the server. These structures include both heterodimer (HD) and protein-ligand (PL) complexes. The visualization aims to provide users with a comprehensive understanding of the relationships and similarities between different pockets. TMAP achieves this by displaying a subset of edges from a graph representing the pockets. These edges, which correspond to similarities between pockets, are structured in a tree-like fashion, forming a connected graph where each vertex represents a pocket. The visualization algorithm minimizes the sum of the edge weights, ensuring an optimal representation of pocket similarity. In essence, TMAP offers a clustered view of pockets based on their similarities, enabling users to identify groups of pockets with comparable characteristics or functional properties. This approach facilitates the exploration and analysis of protein structures and their associated pockets, thereby aiding researchers in understanding the structure-function relationships of proteins and guiding drug discovery efforts.
On the top panel on the website, go to “Query pockets”, then under the “Navigate the PPI pocketome” section on the right, click Go to Pocketome. This will display the pocketome visualization of all the PPIs on the server.
No, it can present hypotheses for both drug and epitope repurposing but it is not repurposed.
The HD dataset is a set of heterodimers. The PL dataset is a set of proteins with ligands associated with one or several heterodimers. These are taken from the RCSB PDB website.
Yes, for example MDM2 (https://www.uniprot.org/uniprotkb/Q00987/entry#names_and_taxonomy)
User login is not mandatory to access the content of PIE. It's possible to explore all data without authentication. However, to add pharmacological data and compounds to the compounds section of IPPI-DB, having an account is necessary for traceability and recognition purposes.
Using FoldX, critical hot spots are identified as locations where substituting alanine leads to a substantial rise in free binding energy, at least 1.5 kcal/mol (free enthalpy). Warm hot spots, on the other hand, are sites where alanine substitutions cause a noticeable increase in binding energy, ranging from 0.5 kcal/mol to 1.5 kcal/mol. Essentially, hot spots are delineated based on the energetic impact of amino acid side chains on protein binding.