ArticleNucleic acids research2012
PoSSuM: a database of similar protein-ligand binding and putative pockets.
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 28 papers.
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Who cites it
28 citing papers in PubMed, 55 citations in OpenAlex.
- Structural and Dynamics Analyses of β-Lactam Inhibition ofACS chemical biology · 2026Article
- Exploring Binding Sites on Proteins for Function Prediction Using the PoSSuM Databases.Methods in molecular biology (Clifton, N.J.) · 2025Article
- VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites.Scientific reports · 2024Article
- Bayesian Optimization in the Latent Space of a Variational Autoencoder for the Generation of Selective FLT3 Inhibitors.Journal of chemical theory and computation · 2024Article
- PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins.Journal of chemical information and modeling · 2023Article
- Protein-protein interaction prediction methods: from docking-based to AI-based approaches.Biophysical reviews · 2022Review
- A multilayer dynamic perturbation analysis method for predicting ligand-protein interactions.BMC bioinformatics · 2022Article
- Discovery of novel SARS-CoV-2 inhibitors targeting the main protease MAntiviral research · 2022Article
- Article
- Computational Methods for Drug Repurposing.Advances in experimental medicine and biology · 2022Article
- Review
- CavBench: A benchmark for protein cavity detection methods.PloS one · 2019Article
- Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot.Biophysics and physicobiology · 2019Article
- Novel Computational Approach to Predict Off-Target Interactions for Small Molecules.Frontiers in big data · 2019Article
- A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).PLoS computational biology · 2018Article
- In silico identification and experimental validation of hits active against KPC-2 β-lactamase.PloS one · 2018Article
- Assessing the similarity of ligand binding conformations with the Contact Mode Score.Computational biology and chemistry · 2016Article
- PDID: database of molecular-level putative protein-drug interactions in the structural human proteome.Bioinformatics (Oxford, England) · 2016Article
- Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets.Biophysics and physicobiology · 2016Article
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ~33,000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/.
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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.