E3 Ligase Ligandalyzer: A Structure-First, Ligand-Centric Platform for E3 Ligase Recruiter Selection
- 1University of Miami Miller School of Medicine
Abstract
Here, we present E3 Ligase Ligandalyzer Version 1.0, a freely accessible, recruiter-centric web platform for comparative exploration of experimentally resolved E3 ligase-recruiter complexes. The locked Version 1.0 dataset spans 35 E3 ligases, 604 reconciled recruiter entities, and 1,372 active structure-specific recruiter instances across 685 experimentally resolved PDB structures. Recruiters are linked to normalized chemical representations and analyzed using cheminformatics and structure-based workflows to compute physicochemical descriptors, scaffold relationships, aligned binding-pocket views, and solvent-accessible surface area patterns relevant to linker attachment. The platform integrates recruiter-entity, recruiter-instance, scaffold, and ligase views, allowing users to compare experimentally grounded chemical and structural observations without imposing predictive rankings. The platform supports direct transition into downstream degrader-design workflows, including integration with PROTAC Builder (protacbuilder.com). E3 Ligase Ligandalyzer is freely available at https://e3ligandalyzer.com, and the associated code and dataset-generation scripts are available at https://github.com/schurerlab/E3-Ligandalyzer-Scripts.
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BibTeX
@misc{schulz2026ligase,
title = {{E3 Ligase Ligandalyzer: A Structure-First, Ligand-Centric Platform for E3 Ligase Recruiter Selection}},
author = {J. M. Schulz and M. Bardhan and R. Reynolds and G. Leroy and D. Reinberg and S. C. M. Schurer},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.07.757351},
url = {https://www.biorxiv.org/content/10.64898/2026.10.07.757351v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - E3 Ligase Ligandalyzer: A Structure-First, Ligand-Centric Platform for E3 Ligase Recruiter Selection
AU - J. M. Schulz
AU - M. Bardhan
AU - R. Reynolds
AU - G. Leroy
AU - D. Reinberg
AU - S. C. M. Schurer
PY - 2026
DA - 2026/10/07
PB - bioRxiv
DO - 10.64898/2026.10.07.757351
UR - https://www.biorxiv.org/content/10.64898/2026.10.07.757351v1
AB - Here, we present E3 Ligase Ligandalyzer Version 1.0, a freely accessible, recruiter-centric web platform for comparative exploration of experimentally resolved E3 ligase-recruiter complexes. The locked Version 1.0 dataset spans 35 E3 ligases, 604 reconciled recruiter entities, and 1,372 active structure-specific recruiter instances across 685 experimentally resolved PDB structures. Recruiters are linked to normalized chemical representations and analyzed using cheminformatics and structure-based workflows to compute physicochemical descriptors, scaffold relationships, aligned binding-pocket views, and solvent-accessible surface area patterns relevant to linker attachment. The platform integrates recruiter-entity, recruiter-instance, scaffold, and ligase views, allowing users to compare experimentally grounded chemical and structural observations without imposing predictive rankings. The platform supports direct transition into downstream degrader-design workflows, including integration with PROTAC Builder (protacbuilder.com). E3 Ligase Ligandalyzer is freely available at https://e3ligandalyzer.com, and the associated code and dataset-generation scripts are available at https://github.com/schurerlab/E3-Ligandalyzer-Scripts.
ER -