PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX
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Abstract
Summary: The identification and characterization of interfaces in protein complexes is crucial for understanding the mechanisms of molecular recognition. These interfaces are also attractive targets for protein inhibition. However, targeting protein interfaces can be challenging for large interfaces that consist of multiple interacting regions. We present PICKLUSTER [Protein Interface C(K)luster]—a program for identifying “sub-interfaces” in protein–protein complexes using distance clustering. The division of the interface into smaller “sub-interfaces” offers a more focused approach for targeting protein–protein interfaces. Availability and implementation: PICKLUSTER is implemented as a plug-in for the molecular visualization program UCSF ChimeraX 1.4 and subsequent versions. It is freely available for download in the ChimeraX Toolshed and https://gitlab.com/topf-lab/pickluster.git.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
A structural biology community assessment of AlphaFold2 applications
Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00849-w · Cited by 675 · see citing works
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Genz, L. R., Nair, S., Nagar, N., & Topf, M. (2025) · Protein Science · doi:10.1002/pro.70327 · Cited by 17 · see citing works
Self-citation
- Authors
- Genz, L. R., Mulvaney, T., Nair, S., & Topf, M.
- Affiliations
- Leibniz Institute of Virology (LIV) (DE)
- Corresponding author
- Topf, Maya
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-10-16
- Volume
- 39
- Issue
- 11
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC10629935
- OpenAlex
- W4387691791
- Cited by
- 14
- References
- 2
- Citations by year
- 2026: 5 · 2025: 9
- FWCI
- 1.25
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- cooperation of Leibniz Institute of Virology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein interfaces, distance clustering, protein-protein complex, molecular recognition, molecular visualization
- MeSH terms
- Proteins, Software, Cluster Analysis
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