ArticleNucleic acids research2012
Pocketome: an encyclopedia of small-molecule binding sites in 4D.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
79 citing papers in PubMed, 179 citations in OpenAlex.
- More protein-ligand data are needed for AlphaFold-like models to enable drug discovery.Current opinion in structural biology · 2026Review
- Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities.bioRxiv : the preprint server for biology · 2026Article
- Cheminformatic analysis of protein surfaces provides binding site insights and informs identification strategies.Future medicinal chemistry · 2025Article
- Systematic Exploration of Small-Molecule Binding via a Large Language Model Trained on Textualized Protein-Ligand Interactions.Molecules (Basel, Switzerland) · 2025Article
- Discovery of small molecule probes targeting the 5' stem-loop in the yeast U4/U6 snRNA.bioRxiv : the preprint server for biology · 2025Article
- Towards a comprehensive view of the pocketome universe-biological implications and algorithmic challenges.PLoS computational biology · 2025Article
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
- TcSR62, an RNA-binding protein, as a new potential target for anti-trypanocidal agents.Frontiers in microbiology · 2025Article
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- Synergy of Mutation-Induced Effects in Human Vitamin K Epoxide Reductase: Perspectives and Challenges for Allo-Network Modulator Design.International journal of molecular sciences · 2024Article
- Crystallographic Fragment Screening on theACS omega · 2023Article
- Expanding Training Data for Structure-Based Receptor-Ligand Binding Affinity Regression through Imputation of Missing Labels.ACS omega · 2023Article
- Effect of Colchicine Binding Site Inhibitors on the Tubulin Intersubunit Interaction.ACS omega · 2023Article
- Data-driven analysis and druggability assessment methods to accelerate the identification of novel cancer targets.Computational and structural biotechnology journal · 2023Review
- 1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes.Protein science : a publication of the Protein Society · 2023Article
- Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening.Molecules (Basel, Switzerland) · 2022Review
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- A new microtubule-stabilizing agent shows potent antiviral effects against African swine fever virus with no cytotoxicity.Emerging microbes & infections · 2021Article
- Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision.Journal of cheminformatics · 2021Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The importance of binding site plasticity in protein-ligand interactions is well-recognized, and so are the difficulties in predicting the nature and the degree of this plasticity by computational means. To assist in understanding the flexible protein-ligand interactions, we constructed the Pocketome, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. The multiplicity of pockets within the ensembles adds an extra, fourth dimension to the Pocketome entry data. Within each ensemble, the pockets were carefully classified by the degree of their pairwise similarity and compatibility with different ligands. The core of the Pocketome is derived regularly and automatically from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is complemented by entries built from manually provided seed ligand locations. The Pocketome website (www.pocketome.org) allows searching for the sites of interest, analysis of conformational clusters, important residues, binding compatibility matrices and interactive visualization of the ensembles using the ActiveICM web browser plugin. The Pocketome collection can be used to build multi-conformational docking and 3D activity models as well as to design cross-docking and virtual ligand screening benchmarks.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.