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Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Protein Modifications in the RER

Protein Modifications in the RER

Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Related Experiment Video

Updated: Dec 21, 2025

Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins

Published on: January 8, 2018

RESTful API for iPTMnet: a resource for protein post-translational modification network discovery.

Sachin Gavali¹, Julie Cowart¹, Chuming Chen^1,2

¹Center for Bioinformatics and Computational Biology, 205 Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA.

Database : the Journal of Biological Databases and Curation

|May 13, 2020

Summary

iPTMnet now offers a RESTful API for seamless integration of protein post-translational modification (PTM) data into bioinformatics workflows. This enables automated data access and enhances scientific discovery, connecting PTM sites to signaling pathways.

Keywords:

Cloud Docker Phosphoproteomics Post-Translational Modification RESTful API Rust Web Service iPTMnet

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Last Updated: Dec 21, 2025

Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins

Published on: January 8, 2018

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications

Published on: May 18, 2017

Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

iPTMnet is a valuable resource for protein post-translational modification (PTM) data.
Current iPTMnet website lacks automated data integration capabilities.
Need for streamlined access to PTM data in research pipelines.

Purpose of the Study:

Develop a RESTful API for iPTMnet to enable automated data integration.
Facilitate the incorporation of iPTMnet data into existing bioinformatics tools and pipelines.
Enhance scientific discovery through easier access to PTM information.

Main Methods:

Developed a RESTful API using cloud technologies.
Packaged the iPTMnet API software in Docker containers for redistribution on DockerHub.
Created Python and R packages for user-friendly integration.

Main Results:

Successfully implemented a RESTful API for iPTMnet.
API is readily available via Docker containers and language-specific packages.
Demonstrated a use case connecting PTM sites to kinase signaling pathways.

Conclusions:

The new iPTMnet API significantly improves data accessibility and integration.
Facilitates automated PTM data retrieval for bioinformatics research.
Empowers researchers to conduct more advanced scientific discovery and analysis.