ArticleProtein science : a publication of the Protein Society2008
Robust recognition of zinc binding sites in proteins.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 93 citations in OpenAlex.
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- Neuropeptides: Roles and Activities as Metal Chelators in Neurodegenerative Diseases.The journal of physical chemistry. B · 2021Review
- The potential of putative zinc-binding motifs of haemagglutinin (HA) protein for categorization and prediction of pathogenicity of H5 subtypes of avian influenza virus.Medical hypotheses · 2020Article
- The Identification of Metal Ion Ligand-Binding Residues by Adding the Reclassified Relative Solvent Accessibility.Frontiers in genetics · 2020Article
- Recognizing Ion Ligand-Binding Residues by Random Forest Algorithm Based on Optimized Dihedral Angle.Frontiers in bioengineering and biotechnology · 2020Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Simple Coordination Geometry Descriptors Allow to Accurately Predict Metal-Binding Sites in Proteins.ACS omega · 2019Article
- Predicting protein-ligand binding residues with deep convolutional neural networks.BMC bioinformatics · 2019Article
- Characterizing metal-binding sites in proteins with X-ray crystallography.Nature protocols · 2018Article
- Effect of glycation on human serum albumin-zinc interaction: a biophysical study.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2018Article
- Computational approaches forBioscience reports · 2017Review
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- Direct Binding of the pH-Regulated Protein 1 (Pra1) fromFrontiers in microbiology · 2017Article
- Potential DNA binding and nuclease functions of ComEC domains characterized in silico.Proteins · 2016Article
- Interaction between IGFBP7 and insulin: a theoretical and experimental study.Scientific reports · 2016Article
- Small Molecule Inhibited Parathyroid Hormone Mediated cAMP Response by N-Terminal Peptide Binding.Scientific reports · 2016Article
- Accumulation of cholesterol and increased demand for zinc in serum-deprived RPE cells.Molecular vision · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Metals play a variety of roles in biological processes, and hence their presence in a protein structure can yield vital functional information. Because the residues that coordinate a metal often undergo conformational changes upon binding, detection of binding sites based on simple geometric criteria in proteins without bound metal is difficult. However, aspects of the physicochemical environment around a metal binding site are often conserved even when this structural rearrangement occurs. We have developed a Bayesian classifier using known zinc binding sites as positive training examples and nonmetal binding regions that nonetheless contain residues frequently observed in zinc sites as negative training examples. In order to allow variation in the exact positions of atoms, we average a variety of biochemical and biophysical properties in six concentric spherical shells around the site of interest. At a specificity of 99.8%, this method achieves 75.5% sensitivity in unbound proteins at a positive predictive value of 73.6%. We also test its accuracy on predicted protein structures obtained by homology modeling using templates with 30%-50% sequence identity to the target sequences. At a specificity of 99.8%, we correctly identify at least one zinc binding site in 65.5% of modeled proteins. Thus, in many cases, our model is accurate enough to identify metal binding sites in proteins of unknown structure for which no high sequence identity homologs of known structure exist. Both the source code and a Web interface are available to the public at http://feature.stanford.edu/metals.
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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.