PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles
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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BibTeX
@article{rahali2026pockflex,
title = {{PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles}},
author = {Inés Rahali and Yacine Serir and Kheira Rahali and Delphine Flatters and Leslie Regad and Anne-Claude Camproux},
journal = {Nucleic Acids Research},
year = {2026},
month = jul,
doi = {10.1093/nar/gkag453},
url = {https://hal.science/hal-05802349v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles
AU - Inés Rahali
AU - Yacine Serir
AU - Kheira Rahali
AU - Delphine Flatters
AU - Leslie Regad
AU - Anne-Claude Camproux
PY - 2026
DA - 2026/07/07
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag453
UR - https://hal.science/hal-05802349v1
AB - 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/.
SN - 0305-1048
SN - 1362-4962
ER -