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Updated: May 9, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles
Inés S Rahali1, Yacine Serir2, Kheira Rahali2
1Inserm U1133, CNRS UMR 8251, Université Paris Cité, Rue Hélène Brion, 75013 Paris, France.
Abstract:
PockFlex is a web server designed to analyse pockets across protein structural ensembles and support the reconstruction, characterisation, and prioritisation of recurrent binding site organisations. Applicable to ensembles derived from molecular dynamics simulations, multiple experimental structures, or protein structure predictions, PockFlex detects pockets independently in each conformation, retains those overlapping a user-defined region of interest, and groups them across the ensemble by residue-level similarity. This residue-centred clustering framework identifies recurrent binding site clusters, quantifies residue recurrence and variability, and distinguishes persistent from transient binding site regions across the ensemble. Pocket-level druggability, predicted using the PockDrug workflow, is summarised at the cluster level to support binding site prioritisation under conformational variability while preserving access to individual pocket scores. The web application provides interactive, residue-level insights into pocket organisation, variability, and druggability in structural ensembles. The web server is free and open to all users, without login requirement, at https://pockflex.rpbs.univ-paris-diderot.fr/.
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