This is a beta version

Curious about proteins and their interactome? Start your journey now.

Protein-protein interactions are central to understanding the functional relationship between proteins. We have curated the available information and augmented with context-specific analysis to ease your research journey.

Glance at konnect2prot

This is an indigenously developed web-based application designed by Dr. Samrat Chatterjee and his group, for the identification of triggers (proteins in the interactome) which are possible causal agents between pathological or pathophysiological conditions. konnect2prot (k2p) contains data curated from various databases with multidimensional information to built network relevant to the end user. This platform is also equipped with network algorithms that can further enhances the decision making process.

About Us

Who we are

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Dr. Chatterjee's lab

We study biological systems in their entirety or in fragments through the lens of system biology. The former covers topics such as network biology, machine learning-based drug discovery, and so forth, while the latter covers various differential equation based kinetic models. The group is supervised by Dr. Samrat Chatterjee and consists of post doctoral fellows, PhD student and research fellows. They are mainly from mathematical and computational backgrounds keen to work on biological problems in an interdisciplinary environment.

Read More

Some significant recent publications from the group.

Halder S., Ghosh S., Chattopadhyay, J., Chatterjee, S., Bistability in cell signalling and its significance in identifying potential drug targets. Bioinformatics (Available online 2021)

Sarmah, D T., Bairagi, N., and  Chatterjee, S., Tracing the footsteps of autophagy in computational biology. Briefings in Bioinformatics, Vol. 22(4), 1-19,(2021)

Features

Features that makes us different

Directionality

All the interactions of k2p are causal, i.e. directed.

Context-specificity

The user can construct context-specific networks using various filters like cellular localization, biological process, molecular functions, and pathways.

Triggers

Using voterank algorithm, k2p identifies triggers in the network.

Network topology

Various topological measures are used in k2p to identify important proteins such as bottlenecks, hubs etc.

Structural information

Structural information like apo and holo structures and ligand information is available.

Enrichment analysis

Using Enrichr, k2p does ontological and pathway enrichment.

Disease interactome

The multi-disease landscape of the proteins in the PPI network can be identified.

PTM

The information of PTMs of proteins are available.

Protein classes

We have also provided classes of every protein in PPI network.

Team

Chevaliers behind konnect2prot

Dr. Samrat Chatterjee

Associate professor

He is a Mathematician. He uses mathematical modelling and system biology to understand biological problems. He formulated and supervised the project.

Dr. Shailendra Asthana

Principal Scientist-I

He is a Computational Biophysicist. His main area of research is structural bioinformatics and drug discovery. He helped in the supervision of the project.

Shivam Kumar

PhD Student

He is doing PhD in Computational Biology. His major work domain is to develop pattern recognition algorithms using AI/ML. He designed and developed the web application.

Dipanka Tanu Sharma

Research Fellow

His research focuses in exploring complexity of biological system using mathematical modeling and network biological approaches. He helped in curation and designing the application.

Other contributers: Ekant Sharma, Komal Sharma, Krishna

Acknowledgement

We could not make the difference without them

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Department of Biotechnology

We would like to thank DBT for proving us the finanical support for this project

Funding body by Govt. of India

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Signor 2.0

We would like to thank signor for providing directional relationship of protein pairs

Directional database for PPI

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DisGeNET

We would like to thank disgenet for providing disease information related to protein

Disease database

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Uniprot

We would like to thank uniprot for providing detailed information of protein charaterstics including its functions and pathways.

Protein information database

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Enrichr

We would like to thank Enrichr for providing enrichment score of pathway, functions and diseases.

Protein enrichment webserver

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PDB

We would like to thank PDB for providing structure related information.

Protein structure database

We would also like to pass our gratitude to open source software develpers of Flask, Python, Dash (Plotly), MongoDB.

FAQ

Frequently Asked Questions

What is konnect2prot (k2p)?

k2p is a one-stop junction for identifying the triggers in a PPI network constructed from user-given inputs. It is a web-based application of directional PPI which can be filtered according to user-driven context. Currently, context-specificity is defined as filtering the network through the use of localization, pathways, biological processes, and molecular networks. Additionally, it also displays structural insights into the proteins and their available ligands.

Which organism k2p covers?

Currently it contains only proteins from human interactome.

From which databases does k2p extract the curated data?

k2p extracts causal information data from signor. The cellular localization, pathways, biological process, and molecular function information is curated from UniProt. Disease-based information is curated from DisGeNet and the structural information is curated from the PDB database.

What do you mean by the triggers?

We have identified the influential spreaders in the network and augmented it with other auxiliary information to collectively define them as triggers of any pathological condition. Identifying a set of influential spreaders in complex networks plays a crucial role in effective information spreading which are identified using the voterank algorithm. In this approach, all nodes vote in a spreader in each turn, and the voting ability of neighbors of the elected spreader will be decreased in subsequent turns. During investigation the identified triggers could be explored for various applications such as potential drug targets.

How can I obtain the complete dataset?

k2p only allows the extraction of various network images and statistical information generated from the network. The complete data is available upon request.

Which tool is used for pathways and ontological enrichment?

k2p has used Enrichr for the enrichment of biological pathways and ontological enrichment.

Is it commercial and copyright protected?

k2p is a non-commercial open-access web application for academic purposes only. It is copyright protected under Indian Copyright Dairy No.: 14303/2020-CO/SW and funded by the Department of Biotechnology (DBT) (Ministry of Science and Technology, Govt. of India). Grant number: BT/PR15426/BRB/10/1459/2015.

Do I need permission to use the result/image of k2p in my publication?

No. You only have to cite our publication.

How to cite us?

Our manuscript is currently under communication.

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