ArticleNucleic acids research2015
PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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99 citing papers in PubMed.
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- Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures.Computational and structural biotechnology journal · 2026Article
- Garlic-Derived Phytochemical Candidates Predicted to Disrupt SARS-CoV-2 RBD-ACE2 Binding and Inhibit Viral Entry.Molecules (Basel, Switzerland) · 2025Article
- The sulfur-related metabolic status ofVirulence · 2025Article
- Oncogenic PI3Kα variants reveal graded conformational spectrum with mutation-specific cryptic pockets.bioRxiv : the preprint server for biology · 2025Article
- Structure-Based Insights into Stefin-Mediated Targeting of Fowlerpain-1: Towards Novel Therapeutics forPharmaceuticals (Basel, Switzerland) · 2025Article
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
- Subtractive proteo-genomics and model-based druggability analyses prioritized nitrate reductase-A subunit-α as potential therapeutic target against MDR pneumonia; a homology-based approach.BMC microbiology · 2025Article
- Analysis of raltegravir analogs to enhance inhibitory efficiency against HIV integrase.Scientific reports · 2025Article
- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
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- Unveiling the therapeutic potential ofHeliyon · 2024Article
- A Tripeptide (Ser-Arg-Pro, SRP) fromMarine drugs · 2024Article
- Structural basis of p53 inactivation by cavity-creating cancer mutations and its implications for the development of mutant p53 reactivators.Cell death & disease · 2024Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Predicting protein pocket's ability to bind drug-like molecules with high affinity, i.e. druggability, is of major interest in the target identification phase of drug discovery. Therefore, pocket druggability investigations represent a key step of compound clinical progression projects. Currently computational druggability prediction models are attached to one unique pocket estimation method despite pocket estimation uncertainties. In this paper, we propose 'PockDrug-Server' to predict pocket druggability, efficient on both (i) estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure) and (ii) estimated pockets based solely on protein structure information (based on amino atoms that form the surface of potential binding cavities). PockDrug-Server provides consistent druggability results using different pocket estimation methods. It is robust with respect to pocket boundary and estimation uncertainties, thus efficient using apo pockets that are challenging to estimate. It clearly distinguishes druggable from less druggable pockets using different estimation methods and outperformed recent druggability models for apo pockets. It can be carried out from one or a set of apo/holo proteins using different pocket estimation methods proposed by our web server or from any pocket previously estimated by the user. PockDrug-Server is publicly available at: http://pockdrug.rpbs.univ-paris-diderot.fr.
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