ExsA binding site predictions

Overview: Binding site prediction results for selected representative frames extracted from Pseudomonas aeruginosa ExsA monomer and dimer molecular dynamics simulations (DOI 10.5281/zenodo.6704184). Classical small-molecule druggable sites were predicted with Schrödinger SiteMap and the protein structure transformer (PeSTo) [1,2]. Potential protein:protein interaction sites were predicted with Schrödinger SiteMap using modified parameters and PeSTo [1,2]. Allosteric sites were predicted with APOP and PASSer, and cryptic sites with PocketMiner [3,4,5]. ------------------------------------------------------------------------------------------------------------------------------------------------------------ The dataset (ZIP) contains the following folders with the pocket prediction results for the tool [foldername]: apop -- Allosteric site predictions with APOP [3] passer -- Allosteric site predictions with PASSer [4] pesto -- Binding interface predictions with PeSTo [2] pocketminer -- Cryptic pocket predictions with PocketMiner [5] sitemap_default -- Prediction of classical small-molecule druggable sites with SiteMap [1] sitemap_ppi -- Prediction of shallow, hydrophobic binding sites associated with protein:protein interactions (SiteMap [1] with modified parameters) Each folder contains a README-file with further descriptions of the included data. ------------------------------------------------------------------------------------------------------------------------------------------------------------ References: [1] Schrödinger LLC, N. Y., NY (2024) Schrödinger Software Suite. Release 2024-3. SiteMap. [2] Krapp et al. (2023) Nat Commun 14, 2175.[3] Kumar et al. (2023) Bioinformatics 39, btad275.[4] Tian et al. (2023) Nucleic Acids Res. 51, W427-W431.[5] Meller et al. (2023) Nat Commun 14, 1177.