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PICNIC web server for predicting proteins involved in biomolecular condensates
Anna Hadarovich1,2, Maxim Scheremetjew1,2, Hari Raj Singh1
1Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstaße 108, 01307 Dresden, Germany.
Bioinformatics (Oxford, England)
|December 1, 2025
Summary
Researchers can now predict protein involvement in biomolecular condensates using the user-friendly PICNIC web server. This tool, leveraging machine learning and AlphaFold2 models, offers high accuracy for identifying proteins in cellular processes and diseases.
Area of Science:
- Molecular Biology
- Biophysics
- Computational Biology
Background:
- Biomolecular condensates are crucial for cellular functions like gene regulation and signaling.
- Dysregulation of these condensates is linked to diseases, including neurodegeneration.
- Predictive computational tools can help characterize proteins involved in condensate formation.
Purpose of the Study:
- To develop an accessible web server for predicting protein involvement in biomolecular condensates.
- To provide a tool for researchers lacking computational expertise.
- To enable large-scale proteome analysis of condensate-forming proteins.
Main Methods:
- Developed the PICNIC (Proteins Involved in CoNdensates In Cells) machine learning algorithm.
- Utilized sequence- and structure-based features from AlphaFold2 models.
- Incorporated Gene Ontology terms for an extended model (PICNIC-GO) for annotated proteins.
Main Results:
- The PICNIC web server accurately predicts proteins involved in biomolecular condensates with approximately 80% accuracy.
- The server provides an easy-to-use interface for researchers without specialized computational skills.
- Enables rapid hypothesis testing for any protein, including designed or mutated sequences.
Conclusions:
- The PICNIC web server democratizes the study of biomolecular condensates.
- Facilitates proteome-wide identification of proteins associated with condensate formation.
- Supports research into the role of condensates in health and disease.
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