AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline

Christian Fellinger; Marion Sappl; Andras Szabadi; Benjamin Merget; Klaus-Jürgen Schleifer; Thierry Langer

AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline

Christian Fellinger (Corresponding author)
, Marion Sappl
, Andras Szabadi
, Benjamin Merget
, Klaus-Jürgen Schleifer
, Thierry Langer

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

AutoPocket2CREST is an automated workflow for preparing protein–ligand binding pockets for CREST conformational sampling. Starting from protein and ligand structures, the method identifies the ligand, constructs a chemically consistent pocket around it, applies optional backbone constraints, and postprocesses CREST conformers to restore structural annotations. AutoPocket2CREST integrates common open-source tools and enables reproducible semiempirical conformational sampling of protein-bound ligands.

Original language	English
Journal	Journal of Chemical Information and Modeling
Publication status	Published - 23 Mar 2026

Austrian Fields of Science 2012

104027 Computational chemistry
301303 Medical biochemistry

Access to Document

https://pubs.acs.org/doi/10.1021/acs.jcim.6c00569Licence: CC BY 4.0

Cite this

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title = "AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline",

abstract = "AutoPocket2CREST is an automated workflow for preparing protein–ligand binding pockets for CREST conformational sampling. Starting from protein and ligand structures, the method identifies the ligand, constructs a chemically consistent pocket around it, applies optional backbone constraints, and postprocesses CREST conformers to restore structural annotations. AutoPocket2CREST integrates common open-source tools and enables reproducible semiempirical conformational sampling of protein-bound ligands.",

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AU - Fellinger, Christian

AU - Sappl, Marion

AU - Szabadi, Andras

AU - Merget, Benjamin

AU - Schleifer, Klaus-Jürgen

AU - Langer, Thierry

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AB - AutoPocket2CREST is an automated workflow for preparing protein–ligand binding pockets for CREST conformational sampling. Starting from protein and ligand structures, the method identifies the ligand, constructs a chemically consistent pocket around it, applies optional backbone constraints, and postprocesses CREST conformers to restore structural annotations. AutoPocket2CREST integrates common open-source tools and enables reproducible semiempirical conformational sampling of protein-bound ligands.

M3 - Article

SN - 1549-9596

JO - Journal of Chemical Information and Modeling

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