ArticleNucleic acids research2013
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- SPSignal: a web tool for structure-assisted prediction of nuclear localization and nuclear export signals in proteins.Nucleic acids research · 2026Article
- Supervised learning of protein variant effects across large-scale mutagenesis datasets.Protein science : a publication of the Protein Society · 2026Article
- Predictive Model for Single-Site Mutations That Change Intrinsically Disordered Protein Binding Energetics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids.bioRxiv : the preprint server for biology · 2025Article
- ATP-Driven Allosteric Regulation of 14-3-3: Positive Modulation of ATP Hydrolysis and Negative Regulation of Peptide Binding.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Chemoproteomics identifies protein ligands for monoacylglycerol lipids.Communications chemistry · 2025Article
- Cell envelope polysaccharide modifications alter the surface properties and interactions ofmBio · 2025Article
- ExploreTurns: A web tool for the exploration, analysis, and classification of beta turns and structured loops in proteins; application to beta-bulge and Schellman loops, Asx helix caps, beta hairpins, and other hydrogen-bonded motifs.Protein science : a publication of the Protein Society · 2025Article
- Repurposing FDA-Approved Drugs Against Potential Drug Targets Involved in Brain Inflammation Contributing to Alzheimer's Disease.Targets (Basel) · 2024Article
- Neurotransmitter recognition by human vesicular monoamine transporter 2.Nature communications · 2024Article
- Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention.Journal of chemical information and modeling · 2024Article
- Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain.Nature communications · 2024Article
- Genome mining ofFrontiers in microbiology · 2024Article
- ANN based prediction of ligand binding sites outside deep cavities to facilitate drug designing.Current research in structural biology · 2024Article
- DL-TCNN: Deep Learning-based Temporal Convolutional Neural Network for prediction of conformational B-cell epitopes.3 Biotech · 2023Article
- KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities.Nucleic acids research · 2023Article
- Molecular docking in organic, inorganic, and hybrid systems: a tutorial review.Monatshefte fur chemie · 2023Review
- HyperCys: A Structure- and Sequence-Based Predictor of Hyper-Reactive Druggable Cysteines.International journal of molecular sciences · 2023Article
- Computational Biology of BRCA2 in Male Breast Cancer, through Prediction of Probable nsSNPs, and Hit Identification.ACS omega · 2022Article
22 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water. We consider the non-bulk waters to occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation of cavity sizes is statistically superior to estimates made by CASTp and VOIDOO, and on par with McVol over a data set of 40 cavities. Our calculated cavity volumes correlated best with the experimentally determined destabilization of 34 mutants from five proteins. Some of the cavities identified are capable of binding small molecule ligands. In this study, we have enhanced our depth-based predictions of binding sites by including evolutionary information. We have demonstrated that on a database (LigASite) of ∼200 proteins, we perform on par with ConCavity and better than MetaPocket 2.0. Our predictions, while less sensitive, are more specific and precise. Finally, we use depth (and other features) to predict pKas of GLU, ASP, LYS and HIS residues. Our results produce an average error of just <1 pH unit over 60 predictions. Our simple empirical method is statistically on par with two and superior to three other methods while inferior to only one. The DEPTH server (http://mspc.bii.a-star.edu.sg/depth/) is an ideal tool for rapid yet accurate structural analyses of protein structures.
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